Introduction to Biomolecular Simulation using CHARMM

Introduction to Biomolecular Simulation 

using CHARMM 

Yuk Sham 

Supercomputing Institute Consultant 

Phone: (612) 627-7472 

Email: shamy@msi.umn.edu

• Introduction to Molecular Dynamic Simulation 

• Access to Charmm 

• Input files 

• Getting started: Preparing your system 

• Script for MD Simulation 

Outline

What is Molecular Dynamic (MD) simulation ?

What is Molecular Dynamics (MD) Simulation 

• Based on Newton’s classical equations of motion 

• What can MD simulation provide ? 

– Dynamic behavior of system with time 

– Conformational flexibility of large molecules 

– Provide accessible conformation of states 

– Give the timescale of structural fluctuation 

– The MD trajectory can be used to calculate 

thermodynamic properties 

lim 

T →∞ 

A( 

t) 

= 

A

How does MD works 

1) Get a properly energy minimized conformation 

2) Give each atom a randomly assigned velocity based on 

Maxwell-Boltzmann distribution for the temperature of 

interest ( 0 0 ) 

3) Based on a given potential energy function (forcefields), 

calculate the forces on all atoms 

4) With position, velocity and force, use Newton’s equation 

to predict the position and velocity of an atom at a new 

time. 

5) Use the new atomic position to recalculate the forces. 

6) Keep repeating step (4) and (5) to generate the 

dynamical events of your system over time 

r r r r r r 

r r r 

r v , F → r , v , F →→→→ r , v , F 

,v 

r 

r 

( r r r 

r ) 

0 , v0, 

F0 

( r r r 

) r r 

r0 

, v0, 

F0 

→ ( rt 

1, 

vt1) 

r r 

r 

( r ) ( r r ) 

t1 

, vt1 

→ rt 

1, 

vt1, 

Ft1 

( ) ( ) ( ) 

t1, 

t1 

t1 

t2 

t2 

t2 

T 

T 

T 

( ) 

0 

r r

Forcefields 

• Describes the system in the atomic level 

• An empirical energy function use to 

describe your system 

• Consist of bonded and non-bonded 

interactions 

• Bonded interactions: e.g. bonds, angle, 

dihedral and improper torsion 

• Non-bonded interactions: e.g. Van der 

Waals and coulombic.

E 

= 

= 

+ 

+ 

+ 

Typical example of a forcefield 

E 

1 

2 

1 

2 

1 

2 

bond 

∑ 

bonds 

∑ 

∑ 

+ 

K 

angles 

∑ 

φ 

dihedrals 

non−bonds 

b 

K 

E 

K 

angle 

+ 

E 

( b − b ) 

θ 

0 

( θ −θ 

) 

0 

2 

[ 1+ 

cos( 

nφ 

−) 

] 

⎧ ⎡⎛σ 

⎞ 

⎪4ε 

⎢⎜ 

⎟ 

⎪ ⎢ 

⎨ ⎣⎝ 

r ⎠ 

⎪ q1q2 

⎪+ 

⎩ Dr 

dihedral 

2 

12 

+ 

E 

2 

vdw 

+ 

6 

⎛σ 

⎞ ⎤⎫ 

− ⎜ ⎟ ⎥⎪ 

⎝ r ⎠ ⎥⎦ 

⎪ 

⎬ 

⎪ 

⎪ 

⎭ 

E 

elec 

+ 

- 

(short range) 

(long range)

Couple more equations to keep in mind 

N 

∑ 

i= 

1 

1 

2 

m 

i 

v 

2 

i 

F 

F 

= 

= 

= 

3 

2 

NkT 

∂E 

− 

∂r 

m&r 

&

Then what is minimization ? 

• Use to refine the initial 

conformation of a molecule 

• Great to remove bad bonds, angles, 

torsion etc as well as clashes 

between atoms 

• Knows only about the atomic 

positions and the potential energy 

function

How does minimization works ? 

• Remember calculus !! Find me the 

minima to a function - in this 

case your potential energy 

function (forcefield) 

• First order method 

F 

= 

− 

∂E 

∂r 

• Repeatedly move the coordinates 

in your system in such a way that 

the derivative goes to zero 

(minimum) 

An illustration of how 

steepest descent (SD) work 

(*SD only finds local 

minimum)

Fixing atoms 

• Stop atom(s) from moving during 

minimization and/or MD 

• Certain atomic interactions are excluded 

Restraining atoms 

• Keep atom(s) from moving away from a 

defined position, distance, angle etc during 

minimization or MD 

• Calculation include additional energy terms 

to the existing potential energy function

Charmm

Chemistry hemistry at Harvard Harvard 

Macromolecular 

acromolecular 

Mechanics echanics (CHARMM ( CHARMM) 

• MD core 

• Implicit Solvent Model (GB, PB, EEF1) 

• Interface to GAMES for QM/MM 

• Free Energy Perturbation Methods 

• Replica Exchange Methods 

• Monte Carlo and Genetic Algorithms 

• Analysis tool 

• Internal Parser for scripting

Availability 

• Academics/Government (CHARMM) $ 

– http://www.charmm.org 

• Commercial (CHARMm) $$$$$$$$$$ !!! 

– Accelrys Inc.

Licensing 

MSI research licenses 

- 8 restricted licenses to MSI researchers 

- only 8 single CPU job, 4 two CPU job etc ….. 

can be run at any given time. 

Group research licenses 

- Individual research group can purchase 

Charmm at academic price. 

- Unrestricted to group members and 

collaborators. 

- Unlimited usage.

uild 

doc 

exec 

lib 

Source tree 

Version 

source 

support 

test 

tool 

toppar

Compiling Charmm 

install.com [ ] 

= { alpha, alphamp, cm5, convex, cray, cspp, dec, gnu, 

gws, hal, hpux, ibmrs, ibmsp, intel, sgi, stardent, sun, t3d, terra } 

= { reduced, small, medium, large} 

= { 1, 2, FULL, LITE, F77, G77, P, M, S, 64, Q, C, X, G} 

SGI: 

install.com sgi large FULL M 64 

IBM SP3: 

install.com ibmsp3 large FULL

When parallel version does not compile 

= { 1, 2, FULL, LITE, F77, G77, P, M, S, 64, Q, C, X, G} 

2 to halt after making installation utilities 

Check pref.dat in build// 

IBMSP 

UNIX 

SCALAR 

CMPI 

MPI 

LARGE 

PUTFCM 

FCMDIR=fcm 

OLDDYN 

PBOUND 

PARALLEL 

GENCOMM 

PARAFULL 

SYNCHRON 

. 

. 

END

When things does not compile 

• Check Makefile_hosts in build//Makefile_hosts 

• ROOT = rootdir 

• SRC = $(ROOT)/source 

• FLX = $(ROOT)/tool/preflx 

• LIB = $(ROOT)/lib/ibmsp3 

• EXEC = $(ROOT)/exec/ibmsp3 

• FC = mpxlf -qalign=4k -qarch=auto -qcache=auto -qtune=auto -qmaxmem=-1 

• CC = cc -Dnographics -Dnographics -Dibmrs 

• . 

• . 

• . 

• VPATH = fcm 

• FC0 = $(FC) -c -g 

• FC1 = $(FC) -c -O -g 

• FC2 = $(FC) -c -O3 -qarch=pwr3 -qtune=pwr3 

• FC3 = $(FC) -c -O3 -qarch=pwr3 -qtune=pwr3 

• FCR = $(FC) -c -O3 -qstrict -g 

• FCD = $(FC) -c -no -g 

• FCRD = $(FC) -c -no -g 

• LIBS = \ 

• $(LIB)/adumb.a \ 

• . 

• .

Platforms 

-SGI, IBM, SUN 

Where find CHARMM at MSI 

-BSCL, VWL, SDVL 

-Altix 

-SP, regatta 

Accessing CHARMM 

Running the executable 

/usr/local/charmm/c30b2/exec/ibmsp3/charmm 

/usr/local/charmm/c30b2/exec/sgi-par/charmm 

Charmm Documentation 

/usr/local/charmm/c30b2/doc 

Current version is c30b2

Interactively 

/usr/local/charmm/c29b2/exec/sun-ser/charmm 

Non-interactive Serial 

Running CHARMM 

/usr/local/charmm/c29b2/exec/sun-ser/charmm < file.inp > file.out & 

In parallel (with MPI on SGI) 

mpirun –np 4 /usr/local/charmm/c29b2/exec/sgi-ser/charmm < file.inp 

> file.out & 

np is the number of processors

Online documentation at www.charmm.org

Documentaton 

CHARMM Element doc/cons.doc 1.1 

 

File: Cons, Node: Top, Up: (chmdoc/commands.doc), Next: Harmonic Atom 

CONSTRAINTS 

The following forms of constraints are available in CHARMM: 

* Menu: command 

* Harmonic Atom:: "CONS HARM" Hold atoms in place 

* Dihedral:: "CONS DIHE" Hold dihedrals near selected values 

* Internal Coord:: "CONS IC“ Holds bonds, angles and 

dihedrals near table values 

* Quartic Droplet:: "CONS DROP" Puts the entire molecule in a cage 

about the center of mass 

* RMSD restraints: "RMSD" Holds atoms in place relative to 

reference structure 

. 

. 

File: Cons, Node: Harmonic Atom, Up: Top, Next: Dihedral, Previous: Top 

Holding atoms in place

[SYNTAX CONS HARMonic] 

Syntax: 

Documentaton 

CONS HARMonic {[ABSOlute] absolute-specs force-const-spec coordinate-spec } 

{ BESTfit bestfit-specs force-const-spec coordinate-spec} 

{ RELAtive bestfit-specs force-const-spec 2nd-atom-selection} 

{ CLEAr} 

force-const-spec ::= { FORCE real } atom-selection [MASS] 

{ WEIGhting } 

absolute-specs ::= [EXPOnent int] [XSCAle real] [YSCAle real] [ZSCAle real] 

bestfit-specs ::= [ NOROtation ] [ NOTRanslation ] 

coordinate-spec::= { [MAIN] } 

{ COMP } 

{ KEEP }

One useful tip to find things in 

documentation and test cases !! 

cd /usr/local/charmm/c30b2/test 

grep -i “diffusion” */*.inp 

cd /usr/local/charmm/c30b2/doc 

grep -i “diffusion” *.doc 

This will find “case case-insensitively 

insensitively” in all 

the documentations and test cases that 

has the word “diffusion diffusion”

CHARMM INPUT FILES

What is in the CHARMM input 

• Topology file – predefined topological library 

• Parameter file – predefined parameters 

• PDB or CRD file – Spatial Atomic coordinates 

• PSF file – Topological definition of system 

• RST file – Latest velocity and coordinate from MD

Topology File 

Topology File 

• These files are a beta release; additional parameter development 

* and testing may lead to alteration of the contents. 

* 22 1 

MASS 1 H 1.00800 ! polar H 

MASS 2 HC 1.00800 ! N-ter H 

MASS 11 C 12.01100 ! carbonyl C, peptide backbone 

MASS 12 CA 12.01100 ! aromatic C 

MASS 13 CT1 12.01100 ! aliphatic sp3 C for CH 

. 

. 

. 

RESI GLY 0.00 

GROUP 

ATOM N NH1 -0.47 ! | 

ATOM HN H 0.31 ! N-H 

ATOM CA CT2 -0.02 ! | 

ATOM HA1 HB 0.09 ! | 

ATOM HA2 HB 0.09 ! HA1-CA-HA2 

GROUP ! | 

ATOM C C 0.51 ! | 

ATOM O O -0.51 ! C=O 

! | 

BOND N HN N CA O C C CA 

BOND C +N CA HA1 CA HA2 

IMPR N -C CA HN C CA +N O 

DONOR HN N 

ACCEPTOR O C 

IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 

IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 

IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 

IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 

IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 

IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 

IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817

BONDS 

! 

!V(bond) = Kb(b - b0)**2 

! 

!Kb: kcal/mole/A**2 

!b0: A 

! 

!atom type Kb b0 

! 

Parameter File 

C C 600.000 1.3350 ! ALLOW ARO HEM 

CA CA 305.000 1.3750 ! ALLOW ARO 

ANGLES 

! 

!V(angle) = Ktheta(Theta - Theta0)**2 

! 

!V(Urey-Bradley) = Kub(S - S0)**2 

! 

!Ktheta: kcal/mole/rad**2 

!Theta0: degrees 

!Kub: kcal/mole/A**2 (Urey-Bradley) 

!S0: A 

! 

!atom types Ktheta Theta0 Kub S0 

! 

CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO 

CE1 CE1 CT3 48.00 123.50 ! 

CE1 CT2 CT3 32.00 112.20 ! 

. 

. 

.

header 

sequence 

sec. struct 

structure 

info. 

connectivity 

PDB file format 

HEADER CALCIUM-BINDING PROTEIN 29-SEP-92 1CLL 2 

COMPND CALMODULIN (VERTEBRATE) 1CLL 3 

REMARK 1 REFERENCE 1 1CLL 13 

REMARK 1 AUTH W.E.MEADOR,A.R.MEANS,F.A.QUIOCHO 1CLL 14 

RORIGX2 0.000000 0.018659 0.001155 0.00000 1CLL 143 

. 

. 

SEQRES 1 148 ALA ASP GLN LEU THR GLU GLU GLN ILE ALA GLU PHE LYS 1CLL 110 

SEQRES 2 148 GLU ALA PHE SER LEU PHE ASP LYS ASP GLY ASP GLY THR 1CLL 111 

SEQRES 3 148 ILE THR THR LYS GLU LEU GLY THR VAL MET ARG SER LEU 1CLL 112 

. 

. 

HELIX 5 V ALA 102 ASN 111 1 1CLL 134 

HELIX 6 VI ASP 118 ALA 128 1 1CLL 135 

HELIX 7 VII TYR 138 THR 146 1 1CLL 136 

SHEET 1 S1 2 ILE 27 THR 29 0 1CLL 137 

SHEET 2 S1 2 ILE 63 PHE 65 -1 N ILE 63 O ILE 27 1CLL 138 

. 

. 

ATOM 1 N LEU 4 -6.873 21.082 25.312 1.00 49.53 1CLL 148 

ATOM 2 CA LEU 4 -6.696 22.003 26.447 1.00 48.82 1CLL 149 

ATOM 3 C LEU 4 -6.318 23.391 25.929 1.00 46.50 1CLL 150 

ATOM 4 O LEU 4 -5.313 23.981 26.352 1.00 45.72 1CLL 151 

ATOM 5 N THR 5 -7.147 23.871 25.013 1.00 46.77 1CLL 152 

ATOM 6 CA THR 5 -6.891 25.193 24.428 1.00 46.84 1CLL 153 

. 

. 

. 

CONECT 724 723 1137 1CLL1440 

CONECT 736 735 1137 1CLL1441

CRD file format 

*This is a box of 125 water molecules in the experimental 

*geometry. The box was equilibrated previously by Monte Carlo 

*for the MCY potential. It is probably appropiate for starting 

*configurations for all 3-site water models. The box length 

*is 15.5516 A and the temperature and density are 300 K and 

*0.0334 A**-3. 

* 

375 

1 1 TIP3 OH2 -5.76008 3.27789 -3.46973 

2 1 TIP3 H1 -5.57742 3.20183 -2.53321 

3 1 TIP3 H2 -5.78382 4.22062 -3.63382 

4 2 TIP3 OH2 5.34253 0.76916 0.26836 

5 2 TIP3 H1 5.57754 1.03356 -0.62107 

6 2 TIP3 H2 6.17167 0.50533 0.66729 

7 3 TIP3 OH2 -2.67359 0.49251 -3.75320 

8 3 TIP3 H1 -2.64318 1.40181 -3.45575

PSF file format 

PSF 

2 !NTITLE 

* Insight II-generated PSF for GB12_ALL using the charmm22.cfrc forcefield 

* Produced on Tue Sep 17 14:23:27 2002 by shamy 

10869 !NATOM 

1 GB12 1 MET N 56 -3.000000E-01 14.0070 0 

2 GB12 1 MET HN1 2 3.300000E-01 1.0080 0 

7537 !NBONDS: bonds 

. 

4889 !NTHETA: angles 

. 

2262 !NPHI: dihedrals 

. 

136 !NIMPHI: impropers 

. 

0 !NDON: donors 

. 

0 !NACC: acceptors 

. 

0 !NNB 

. 

3794 0 !NGRP, NST2 

.

CHARMM COMMANDS and OUTPUT

What is in the CHARMM MD script 

open read unit 21 card name top_all22_prot_na.rtf 

read rtf unit 21 card 

close unit 21 

open read unit 20 card name par_all22_prot_na.prm 

read para unit 20 card 

close unit 20 

open read unit 20 card name 2gb1.psf 

read psf unit 20 card 

close unit 20 

open read unit 20 card name 2gb1.crd 

read coor unit 20 card 

close unit 20 

set 7 45.000000 

set 8 45.000000 

set 9 55.000000 

crystal define tetr @7 @8 @9 90.0 90.0 90.0 

crystal build noper 0 cutoff 20.0 

image byres select all end

What is in the CHARMM MD script (cont’d) (cont d) 

update atom vdw vshift cdie eps 1.0 cutnb 12.0 ctofnb 10.0 - 

inbfrq 25 imgfrq 50 ihbfrq 50 

shake bonh tol 1.0e-6 mxit 500 

open read unit 30 card name equil.rst 

dynamics verl rest - 

timestep 0.001000 nstep 1000 - 

firstt 300.000000 finalt 300.000000 - 

ihtfrq 0 ieqfrq 0 iasors 0 iasvel 1 iscvel 0 ichecw 0 - 

twindh 10.0 twindl -10.0 - 

ntrfrq 1000 iprfrq 50 - 

isvfrq 100 nsavc 100 nsavv 100 nprint 100 - 

iunrea 30 iunwri -1 iuncrd -1 iunvel -1 kunit -1 - 

ewald pmewald kappa 0.34 order 6 - 

fftx 48 ffty 48 fftz 60 

stop

• % charmm 

• 1 

• Chemistry at HARvard Macromolecular Mechanics 

• (CHARMM) - Developmental Version 29b2 February 15, 2003 

• Copyright(c) 1984-2001 President and Fellows of Harvard College 

• All Rights Reserved 

• Current operating system: IRIX64-6.5(IP28)@cirrus.msi.umn.edu 

• Created on 4/ 2/ 3 at 18:36:19 by user: shamy 

• Maximum number of ATOMS: 60120, and RESidues: 72000 

• Current HEAP size: 10240000, and STACK size: 2000000 

• CHARMM> 

start


• stop 

• CHARMM> stop 

• $$$$$$ New timer profile $$$$$ 

• Total time 4.55310 Other: 0.00000 

• NORMAL TERMINATION BY NORMAL STOP 

• MAXIMUM STACK SPACE USED IS 0 

• STACK CURRENTLY IN USE IS 0 

• MOST SEVERE WARNING WAS AT LEVEL 1 

• HEAP PRINTOUT- HEAP SIZE 10240000 

• SPACE CURRENTLY IN USE IS 0 

• MAXIMUM SPACE USED IS 480 

• FREE LIST 

• PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0 

• $$$$$ JOB ACCOUNTING INFORMATION $$$$$ 

• ELAPSED TIME: 4.56 SECONDS 

• CPU TIME: 0.06 SECONDS 

stop

Title/comment/continuation 

Title lines 

All title lines starts with “*” follow by text for title 

Last title line finishes with “*” only 

Comment lines 

All comment lines starts with “!” 

Comments can start anywhere in a line with “!”. All text following “!” 

becomes comment. 

Continuing a line 

Command line can be continued to the next line if it ends with “-”

more charmm_stop.inp 

* Spring 2003 charmm tutorial 

* by me 

* 

stop 

Running charmm 

non-interactively 

non interactively

• charmm < charmm_stop.inp 

• 1 



• RDTITL> * SPRING 2004 CHARMM TUTORIAL 

• RDTITL> * BY ME 

• RDTITL> * 







• FREE LIST 

Running charmm 

non-interactively 

non interactively

Output to file 

• charmm < charmm_stop.inp > charmm_stop.out 

• more charmm_stop.out 

• 1 



• RDTITL> * SPRING 2003 CHARMM TUTORIAL 

• RDTITL> * BY ME 

• RDTITL> * 







• FREE LIST

1) Read in topology and parameter library files 

2) Read in sequence(s) and coordinates 

3) Add missing coordinates 

4) Read in water box and coordinates 

5) Read in ions and coordinates 

6) Remove overlapping water 

7) Create psf, crd and pdb 

Setup files

more charmm_toppar.inp 

• * Membrane System : sys1.inp 

• * Determine the effective cross-sectional area of the protein 

• * 

• !Read topologie 

• open read card unit 1 name ./top_all22_prot.inp 

• read rtf card unit 1 

• close unit 1 

• !Read parameters 

• open read card unit 2 name ./par_all22_prot.inp 

• read param card unit 2 



Read top/par file


• CHARMM> !Read topologie 

• CHARMM> open read card unit 1 name ./top_all22_prot.inp 

• VOPEN> Attempting to open::./top_all22_prot.inp:: 

• OPNLGU> Unit 1 opened for READONLY access to ./top_all22_prot.inp 

Read top/par file 

• CHARMM> read rtf card unit 1 

• MAINIO> Residue topology file being read from unit 1. 

• TITLE> *>>>>>>>>CHARMM22 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS >>>>>>>>>>>>>>>>> AUGUST 1999


• CHARMM> !Read parameters 

• CHARMM> open read card unit 2 name ./par_all22_prot.inp 

• VOPEN> Attempting to open::./par_all22_prot.inp:: 

• OPNLGU> Unit 2 opened for READONLY access to ./par_all22_prot.inp 

• CHARMM> read param card unit 2 

Read top/par file 

• PARAMETER FILE BEING READ FROM UNIT 2 

• TITLE> *>>>> CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS >>>>>>>>>>>>>> AUGUST 1999

more charmm_toppar.inp 

• !Load protein info 

• open read card unit 10 name ./2gb1.pdb 

• read sequ pdb unit 10 

• generate PROT setup first nter last cter 

• rewind unit 10 

• read coord pdb unit 10 


Read PDB file


• CHARMM> !Load protein info 

• CHARMM> open read card unit 10 name ./2gb1.pdb 

• VOPEN> Attempting to open::./2gb1.pdb:: 

• OPNLGU> Unit 10 opened for READONLY access to ./2gb1.pdb 

• CHARMM> read sequ pdb unit 10 

• MAINIO> Sequence information being read from unit 10. 

• TITLE> COORDINATES 

• TITLE> DATE: 4/ 2/ 3 17:43:22 CREATED BY USER: 

• TITLE> * 

Read PDB file 

• RESIDUE SEQUENCE -- 56 RESIDUES 

• MET THR TYR LYS LEU ILE LEU ASN GLY LYS THR LEU LYS GLY GLU THR …... 

• VAL ASP ALA ALA THR ALA GLU LYS VAL PHE LYS GLN TYR ALA ASN ASP ….. 

• GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE THR VAL THR GLU……. 

• ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 19 TITRATABLE GROUPS 

• THE USER MUST PREDETERMINE THE PROTONATION STATE……………. 

• HIS - 0 ASP - 5 GLU - 5 LYS - 6 TYR - 3 

• CHARMM>


• CHARMM> generate PROT setup first nter last cter 

• THE PATCH 'NTER ' WILL BE USED FOR THE FIRST RESIDUE 

• THE PATCH 'CTER ' WILL BE USED FOR THE LAST RESIDUE 

• GENPSF> Segment 1 has been generated. Its identifier is PROT. 

• PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. 

• PSFSUM> Summary of the structure file counters : 

• Number of segments = 1 Number of residues = 56 

• Number of atoms = 855 Number of groups = 263 

• Number of bonds = 861 Number of angles = 1551 

• Number of dihedrals = 2262 Number of impropers = 137 

• Number of HB acceptors = 95 Number of HB donors = 99 

• Number of NB exclusions = 0 Total charge = -4.00000 


Nter is +NH3- N-terminus 

Cter is COO- C-terminus 

Read PDB file


• CHARMM> rewind unit 10 

• REWINDING UNIT 10 

• CHARMM> read coord pdb unit 10 

• SPATIAL COORDINATES BEING READ FROM UNIT 10 

• TITLE> COORDINATES 

• TITLE> DATE: 4/ 2/ 3 17:43:22 CREATED BY USER: 

• TITLE> * 

Read PDB file 

• ** WARNING ** After reading, there are no coordinates for selected atom: 2 1 MET HT1 

• ** WARNING ** After reading, there are no coordinates for selected atom: 3 1 MET HT2 

• ** WARNING ** After reading, there are no coordinates for selected atom: 16 1 MET HE2 

• ** A total of 419 selected atoms have no coordinates 

• *** LEVEL 2 WARNING *** BOMLEV IS 0 

• CHARMM> close unit 10 

• VCLOSE: Closing unit 10 with status "KEEP" 

• CHARMM>

• print coor 

• ic para 

• ic build 

• print coor 

Repair structure

CHARMM> 

CHARMM> print coor 

Repair Structure 

COORDINATE FILE MODULE 

TITLE> * SPRING 2003 CHARMM TUTORIAL 

TITLE> * BY ME 

TITLE> * 

855 

1 1 MET N -14.02500 2.44800 4.87500 PROT 1 1.26000 

2 1 MET HT1 9999.00000 9999.00000 9999.00000 PROT 1 0.00000 

3 1 MET HT2 9999.00000 9999.00000 9999.00000 PROT 1 0.00000 

4 1 MET HT3 9999.00000 9999.00000 9999.00000 PROT 1 0.00000 

5 1 MET CA -13.52900 1.06400 4.74000 PROT 1 0.43000 

6 1 MET HA 9999.00000 9999.00000 9999.00000 PROT 1 0.00000 

7 1 MET CB -13.72800 0.62200 3.25400 PROT 1 1.24000

CHARMM> 

CHARMM> ic para 

CHARMM> ic build 

CHARMM> print coor 

COORDINATE FILE MODULE 

TITLE> * SPRING 2003 CHARMM TUTORIAL 

TITLE> * BY ME 

TITLE> * 

855 

1 1 MET N -14.02500 2.44800 4.87500 PROT 1 1.26000 

2 1 MET HT1 -15.03538 2.48006 4.63066 PROT 1 0.00000 

3 1 MET HT2 -13.49385 3.07122 4.23385 PROT 1 0.00000 

4 1 MET HT3 -13.89565 2.76902 5.85572 PROT 1 0.00000 

5 1 MET CA -13.52900 1.06400 4.74000 PROT 1 0.43000 

6 1 MET HA -14.06392 0.45340 5.45719 PROT 1 0.00000 

7 1 MET CB -13.72800 0.62200 3.25400 PROT 1 1.24000 

Repair Structure

• !Load water info 

• open read card unit 1 name water.crd 

• read sequence coor unit 1 append 

• generate SOLV setup noangle nodihedrals 


• read coor card unit 1 append 


• coor orient norotate select segid solv end 

• !Load ion info 

• open read card unit 1 name ion.pdb 

• read sequence pdb unit 1 append 

• generate ION setup 


• read coor pdb unit 1 append 


• coor orient norotate select segid ion end 

Load water 

and ions


• CHARMM> coor orient norotate select segid solv end 

• SELRPN> 12666 atoms have been selected out of 13521 

• ORIENT THE COORDINATES TO ALIGN WITH AXIS 

• CENTER OF ATOMS BEFORE TRANSLATION 0.09823 

0.09145 0.10042 

• SELECTED COORDINATES TRANSLATED IN THE MAIN SET. 


• Coor orient places the selected atoms to origin 

Load water 

and ions

Remove 

overlapping 

water 

• delete atom sort – 

• select .byres. (segid SOLV .AND. type oh2 .and. - 

• ((.not. (segid SOLV .OR. hydrogen)) .around. 2.8)) end


• CHARMM> delete atom sort - 

• CHARMM> select .byres. (segid SOLV .AND. type oh2 .and. - 

• CHARMM> ((.not. (segid SOLV .OR. hydrogen)) .around. 2.8)) end 

• SELRPN> 1119 atoms have been selected out of 13525 

• Message from MAPIC: Atom numbers are changed. 

• Message from MAPIC: 373 residues deleted. 

• DELTIC: 1119 bonds deleted 

• DELTIC: 373 angles deleted 

• DELTIC: 373 acceptors deleted 

• PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. 

• PSFSUM> Summary of the structure file counters : 

• Number of segments = 3 Number of residues = 3909 

• Number of atoms = 12406 Number of groups = 4116 

• Number of bonds = 12408 Number of angles = 5400 

• Number of dihedrals = 2262 Number of impropers = 137 

• Number of HB acceptors = 3944 Number of HB donors = 99 

• Number of NB exclusions = 0 Total charge = 0.00000 

Water molecules with an O atom that is 2.8 angstrom 

away from another non-water heavy atom is deleted 

Remove 

overlapping 

water

• open write form unit 13 name prowat.crd 

• write coor card unit 13 

• * crd file 

• * 

• open write form unit 13 name prowat.pdb 

• write coord pdb unit 13 

• * pdb file 

• * 

• open write form unit 13 name prowat.psf 

• write psf card unit 13 

• * psf file 

• * 

Write out 

PDB, CRD, PSF 

files

MD scripts

1) Minimization 

2) Heating 

3) Equilibration 

4) MD Simulation (Data collection) 

MD Simulation

1) Read in topology and parameter library files 

2) Read in setup psf and pdb files 

3) Setup Periodic Boundary Condition 

5) Setup Constraint 

6) Setup non-bond parameters 

7) Setup Minimization or MD parameters 

Setup MD Script

• ! PBC parameters 

• ! Cubic box 50 by 50 by 50 angstrom 

• ! Image by residue 

• crystal define cubic @boxx @boxy @boxz 90.0 90.0 90.0 

• crystal build Noper 0 cutoff 20.0 

• imag byres select all end xcen 0.0 ycen 0.0 zcen 0.0 

Minimization 

• ! non-bond parameters 

• ! Group based cutoff for VDW and coulomb interaction with 

• ! switch function. Constant dielectric of 1.0. 

• update group switch cdiel eps 1.0 - ! Electrostatics 

• vgroup vswitch - ! VDW 

• ctonnb 7.0 ctofnb 8.0 cutnb 9.5 cutim 9.5 wmin 1.5 ! cutoffs 

• ! Minimization Steepest Descent 250 steps 

• mini sd nstep 250

• grep 'MINI>' min.out 

• MINI> 0************* 0.00000************* 0.02000 

• MINI> 10 -33946.06346************* 6.29079 0.00896 

• MINI> 20 -37711.96170 3765.89824 6.90017 0.00401 

• MINI> 30 -39049.60687 1337.64516 7.60603 0.00431 

• MINI> 40 -40340.55779 1290.95093 2.69907 0.00193 

• MINI> 50 -41058.88928 718.33149 3.61866 0.00208 

. 

. 

. 

. 

. 

• MINI> 190 -45160.13689 153.43778 1.01040 0.00099 

• MINI> 200 -45288.07310 127.93621 1.80496 0.00107 

• MINI> 210 -45421.91822 133.84512 2.04633 0.00115 

• MINI> 220 -45543.23595 121.31773 2.08479 0.00123 

• MINI> 230 -45683.71771 140.48176 0.67995 0.00055 

• MINI> 240 -45767.66834 83.95063 2.42551 0.00142 

• MINI> 250 -45911.29192 143.62358 0.79346 0.00064 

Minimization

• shake bonh tol 1.0e-6 mxit 500 

• cons harm force 0.3 select segi prot end 

• open write card unit 51 name heat.rst 

• open write file unit 52 name heat.dcd 

• open write file unit 53 name heat.vel 

• open write card unit 54 name heat.ene 

• DYNAMICS start verlet nstep 5000 timestp 0.001 - 

• firstt 50.0 finalt 300.0 - 

• ihtfrq 40 teminc 2 - 

• iasors 1 iasvel 1 iseed 750376231 - 

• ichecw 0 ieqfrq 0 twindh 10.0 twindl 10.0 - 

• inbfrq 20 imgfrq 20 ihbfrq 20 ilbfrq 40 - 

• nprint 100 iprfrq 500 ntrfrq 500 isvfrq 500 - 

• iunrea -1 iunwri 51 iuncrd 52 iunvel 53 kunit 54 - 

• nsavcrd 1000 nsavvelo 1000 - 

• atom vatom vshift cdiel eps 1.0 - 

• cutnb 12.0 ctofnb 11.0 ctonnb 10.0 cutim 12.0 wmin 1.5 - 

• ewald kappa 0.32 - 

• pmewald fftx 48 ffty 48 fftz 48 order 6 

Heating

• more heat.out 

• SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 

• Total heap storage needed = 1029150 

• Fill Ewald table: Number of points= 10000 EWXmin= 0.000000 EWXmax= 3. 

• 680000 

• Fill ERFC table: linear inter has rms error = 0.788209D-08 Maximum error = 0.16 

• 3876D-07 

• Fill ERFC table: cubic spline has rms error = 0.250959D-11 Maximum error = 0.70 

• 3138D-11 

• NONBOND OPTION FLAGS: 

• ELEC VDW ATOMs CDIElec SHIFt VATOm VSHIft 

• BYGRoup NOEXtnd EWALd 

• CUTNB = 12.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 11.000 

• WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 

• NBXMOD = 5 

• EWALD OPTIONS: KAPPA = 0.320 KMAX = 5 KSQMAX = 27 

• Using Pub FFT 

• Real-to-Complex FFT 

• There are 0 atom pairs and 0 atom exclusions. 

• There are 0 group pairs and 0 group exclusions. 

• with mode 5 found 13959 exclusions and 2239 interactions(1-4) 

• found 762 group exclusions. 

• PRNHBD: CUToff Hydrogen Bond distance = 0.5000 Angle = 90.0000 

• CuT switching ON HB dist. = 3.5000 OFf HB dist. = 4.0000 

• CuT switching ON Hb Angle = 50.0000 OFf Hb Angle = 70.0000 

• ACCEptor antecedents included 

• All hydrogen bonds for each hydrogen will be found 

• Hydrogen bonds between excluded atoms will be kept 

Heating

• NSTEP = 5000 NSAVC = 1000 NSAVV = 1000 

• ISCALE = 0 ISCVEL = 0 IASORS = 1 

• IASVEL = 1 ICHECW = 0 NTRFRQ = 500 

• IHTFRQ = 40 IEQFRQ = 0 NPRINT = 100 

• INBFRQ = 20 IHBFRQ = 20 IPRFRQ = 500 

• ILBFRQ = 40 IMGFRQ = 20 ISEED = 750376231 

• ISVFRQ = 500 NCYCLE = 20 NSNOS = 10 

• FIRSTT = 50.000 TEMINC = 2.000 TSTRUC = -999.000 

• FINALT = 300.000 TWINDH = 10.000 TWINDL = -10.000 

• TIME STEP = 2.04548E-02 AKMA 1.00000E-03 PS 

• SHAKE TOLERANCE = 0.10000E-05 

• NUMBER OF DEGREES OF FREEDOM = 25252 

• SEED FOR RANDOM NUMBER GENERATOR IS 750376231 

• GAUSSIAN OPTION IS 1 

• VELOCITIES ASSIGNED AT TEMPERATURE = 62.5000 

Heating

• grep ‘DYNA>' heat.out 

• DETAILS ABOUT CENTRE OF MASS 

• POSITION : 0.11616492 7.37216775E-02 0.11816128 

• VELOCITY : 1.09212028E-03 1.00600816E-03 -4.34573964E-04 

• ANGULAR MOMENTUM : -4355.9163 -1519.1222 -46.369250 

• KINETIC ENERGY : 9.05093000E-02 

• DYNA DYN: Step Time TOTEner TOTKe ENERgy TEMPerature 

• DYNA PROP: GRMS HFCTote HFCKe EHFCor VIRKe 

• DYNA INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers 

• DYNA EXTERN: VDWaals ELEC HBONds ASP USER 

• DYNA IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec 

• DYNA EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil 

• DYNA PRESS: VIRE VIRI PRESSE PRESSI VOLUme 

• ---------- --------- --------- --------- --------- --------- 

• DYNA> 0 0.00000 -43585.36308 1570.64465 -45156.00773 62.59974 

• DYNA PROP> 2.19263 -43584.92724 1571.95195 0.43584 5700.53315 

• DYNA INTERN> 1464.05680 884.91987 10.11565 265.40773 5.84521 

• DYNA EXTERN> 3376.21103 -43027.86061 0.00000 0.00000 0.00000 

• DYNA IMAGES> -169.48296 -2889.03224 0.00000 0.00000 0.00000 

• DYNA EWALD> 548.51920 -246230.51036240605.80296 0.00000 0.00000 

• DYNA PRESS> 13517.54943 -17317.90486 -7414.99887 -8924.81025 125000.00000 

• ---------- --------- --------- --------- --------- --------- 

• UPDECI: Image update at step 20 

• SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000 

• UPDECI: Nonbond update at step 20 

Heating

• grep ‘DYNA>' heat.out 

• DYNA> 0 0.00000 -43585.36308 1570.64465 -45156.00773 62.59974 

• DYNA> 40 0.04000 -44008.08251 1287.21522 -45295.29773 51.30336 

• DYNA> 80 0.08000 -44400.41656 1343.99084 -45744.40741 53.56621 

• DYNA> 100 0.10000 -44400.19780 1382.17874 -45782.37654 55.08823 

• DYNA> 120 0.12000 -44612.07101 1399.63885 -46011.70986 55.78412 

• DYNA> 160 0.16000 -44768.97546 1462.36984 -46231.34530 58.28433 

. 

. 

. 

. 

. 

• DYNA> 4840 4.84000 -35201.02155 7325.29735 -42526.31890 291.95765 

• DYNA> 4880 4.88000 -34961.95062 7499.36887 -42461.31950 298.89546 

• DYNA> 4900 4.90000 -34961.52847 7380.75953 -42342.28800 294.16816 

• DYNA> 4920 4.92000 -34788.61422 7579.91150 -42368.52573 302.10557 

• DYNA> 4960 4.96000 -34712.71220 7492.80754 -42205.51974 298.63395 

• DYNA> 5000 5.00000 -34712.69464 7558.62654 -42271.32118 301.25724 

Heating


• cons harm clear 

• open read card unit 50 name heat.rst 

• open write card unit 51 name equil.rst 

• open write file unit 52 name equil.dcd 

• open write file unit 53 name equil.vel 

• open write card unit 54 name equil.ene 

• DYNAMICS restart verlet nstep 2500 timestp 0.001 - 



• iasors 1 iasvel 1 - 




• iunrea 50 iunwri 51 iuncrd 52 iunvel -1 - 






Equilibration

• grep ‘DYNA>' equil.out 

Equilibration 

• DYNA> 0 5.00000 -32684.09033 7524.24605 -40208.33638 299.88697 

• DYNA> 100 5.10000 -32683.69167 7242.72814 -39926.41982 288.66677 

• DYNA> 200 5.20000 -32683.29060 7026.78314 -39710.07374 280.06004 

• DYNA> 300 5.30000 -32683.10262 6966.34026 -39649.44287 277.65103 

• DYNA> 400 5.40000 -32683.34152 7038.02355 -39721.36507 280.50804 

• DYNA> 500 5.50000 -32683.54636 7018.65906 -39702.20542 279.73625 

• DYNA> 500 5.50000 -32184.08341 7518.12201 -39702.20542 299.64289 

. 

. 

. 

. 

. 

• DYNA> 1800 6.80000 -31785.49212 7418.82587 -39204.31799 295.68533 

• DYNA> 1900 6.90000 -31785.51507 7347.62047 -39133.13554 292.84736 

• DYNA> 2000 7.00000 -31785.21697 7398.66839 -39183.88536 294.88193 

• DYNA> 2000 7.00000 -31785.21697 7398.66839 -39183.88536 294.88193 

• DYNA> 2100 7.10000 -31785.39285 7356.95523 -39142.34808 293.21941 

• DYNA> 2200 7.20000 -31785.31217 7380.62346 -39165.93563 294.16273 

• DYNA> 2300 7.30000 -31785.10303 7300.14193 -39085.24495 290.95506 

• DYNA> 2400 7.40000 -31785.53533 7320.47461 -39106.00993 291.76544 

• DYNA> 2500 7.50000 -31785.34127 7325.52317 -39110.86444 291.96665



• open read card unit 50 name equil.rst 

• open write card unit 51 name simu.rst 

• open write file unit 52 name simu.dcd 

• open write file unit 53 name simu.vel 

• open write card unit 54 name simu.ene 

• DYNAMICS restart verlet nstep 2500 timestp 0.001 - 




• ichecw 1 ieqfrq -1 twindh 10.0 twindl 10.0 - 









Simulation



• open read card unit 50 name heat.rst 

• open write card unit 51 name equil.rst 

• open write file unit 52 name equil.dcd 

• open write file unit 53 name equil.vel 

• open write card unit 54 name equil.ene 

• DYNAMICS restart cpt leap nstep 2500 timestp 0.001 - 












• pmewald fftx 60 ffty 72 fftz 72 order 6 - 

• hoover tmass 1000 reft 300.0 - 

• pconst pint pref 1.0 pmass 500.0 pgamma 20.0 tbath 300.0 

MD with Pressure 

Control (NPT)

Submitting to LoadLeveller 

#!/bin/csh 

#@ initialdir = /homes/r50/shamy/yukdirectory 

#@ wall_clock_limit = 24:00:00 

#@ resources = ConsumableMemory(1000) 

#@ job_type = parallel 

#@ network.MPI = css0,shared,US 

#@ notification = never 

#@ input = simu.inp 

#@ output = simu_1_16_16cpu_regatta.out 

#@ error = simu.err 

#@ node = 1 

#@ tasks_per_node = 16 

#@ queue 

/usr/local/charmm/distrib/c29b2/exec/ibmsp3/charmm

Doing CHARMm in insightII

Setup your system

Setup charmm forcefield

Setup charmm forcefield

Activating CHARMm

Setup your charmm run

Starting charmm run

Your charmm files from insightII 

ls –lt *.inp *.psf *.crd your charmm input 

ls –lt bkgd_job*log your charmm output

Analysist scripts

. 

. 

• !Load protein info 

• open read card formatted unit 10 name @pref.psf 

• read psf card unit 10 


• open read card formatted unit 10 name @pref.crd 

• read coord card unit 10 


• open read unit 20 file name simu_1.dcd 






• open write unit 30 file name cdl.dcd 

• merge coor firstu 20 nunit 6 outputu 30 select segi prot end 


Merge 

files

. 

. 




• open read unit 33 file name simu.dcd 

• traj iread 33 nread 1 

• set 1 1 

• label start 

• traj read 

• incr 1 by 1 

• if 1 lt 1065 goto start 

• open write card unit 15 name snap@1.pdb 

• write coor pdb unit 15 select segi pro end 

• * pdb filE 

• * 



Getting a 

single snapshot

. 

. 




• coor orient 

• coor copy select atom * * ca end comp 

• open unit 10 read file name simu.dcd 

• open write card unit 20 name rms.dat 

• correl maxt 1000000 maxs 1 maxa 347 

• enter aa rms orient 

• traj first 10 

• write aa unit 20 dumb time 


Cα rmsd(time) 

rmsd(time

. 

. 




• open unit 10 read file name md.dcd 

• open write card unit 20 name dist.dat 

• correl maxt 500000 maxs 1 

• enter aa dist PRO 1 SG PRO 5 CE3 

• traj first 10 

• write aa unit 20 dumb time 


Distance(time) 

Distance(time

• Cα atoms 

Distance 

Matrix 

• open unit 1 write form name ca.dmat 

• coor dmat single unit 1 sele atom * * CA end sele atom * * CA end 

• Sidechain atoms 

• define bb select ( type ca .or. type n .or. type c .or. type o ) end 

• define side select ( (.not. bb) .and. (.not. hydrogen) ) end 

• open unit 1 write form name side.dmat 

• coor dmat residue_average single unit 1 cutoff 6.5 select side end - 

• select side end

To get help 

• By mail help@msi.umn.edu 

• Web www.msi.umn.edu 

• Phone 612 626 0802 

• Appointment TBA

Introduction to Biomolecular Simulation using CHARMM

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