Prime User Manual - ISP

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Chapter 11: Command Syntax
Environment Variables
In addition to those used for all Schrödinger software, refinestruct uses the environment
variable PSP_OPLS_VERSION to define the OPLS force field version. The default value is
2005. It can be set to 2001 to use the earlier set of force field parameters for ligands and nonstandard
residues. The OMP_NUM_THREADS environment variable is also supported for
OpenMP multithreaded execution (see above).
Examples
The following is a sample minimization input file:
STRUCT_FILE input-structure.mae
PRIME_TYPE REAL_MIN
SELECT pick
RESIDUE_0 A:1
RESIDUE_1 A:20
RESIDUE_2 A:23
RESIDUE_3 A:26
RESIDUE_4 A:27
RESIDUE_5 A:30
RESIDUE_6 A:31
RESIDUE_7 A:36
RESIDUE_8 A:40
RESIDUE_9 A:42
RESIDUE_10 A:53
USE_RANDOM_SEED false
SEED 0
The arrangement in columns is for ease of reading only—the spacing is not significant.
11.6 ska—Protein Structure Alignment
The SKA program carries out structural alignment of proteins by aligning protein backbones at
different levels of detail.
The ska script provides an interface to the SKA structural alignment program. As with other
computational programs in Prime its operation is controlled through simple input files. The
allowed keywords and their values are discussed in more detail below. The ska script allows
you to run the SKA program in three different modes under Job Control:
• align mode—SKA aligns two or more protein structures to one another.
• dbcreate mode—SKA creates databases for use with scan mode. You should split PDB
files with multiple chains into single-chain files before adding them to the database, as
Prime 2.1 User Manual