MacroModel Reference Manual - ISP

Chapter 4: Operation Codes• Rings (e.g., the one in proline) are treated as rigid.• No disulfide bonds are permitted within the loop or between the loop and the rest of theprotein.• No atoms in the loop can be frozen.Using LOOP usually results in a renumbering of the atoms within the structure such that theloop atoms become the highest numbered atoms in the structure. LOOP tries to make this workby automatically shifting the atom numbers provided in SUBS, FXAT, FXDI, FXBA, FXTA,COMP, and CHIG commands. There are also routines for automatically generating COMP andCHIG atoms for the loop atoms as described for arg3, below. To facilitate subsequent studiesusing the structures generated, a new substructure file, out_filename.sbc, containing theshifted atom numbers is generated automatically. In addition, shifted COMP and CHIGcommands suitable for use in .com files are written in the .log file.If comparison atoms (COMP) are specified explicitly or implicitly (see arg 3) then MSYM mustbe used.arg1arg2arg3−1N-terminus atom number for the loopThis is the atom number for the peptidic Nitrogen atom that joins the loop to theprotein at the N-terminus of the loop. This must be nonzero.C-terminus atom number of the loopThis is the atom number for the peptidic Carbon atom that joins the loop to the proteinat the C-terminus of the loop. This must be nonzero.Type of LOOP GenerationTurn off LOOP and clear out information specified in an earlier loop command. Allother arguments are ignored.0 Generates alternate conformations for the loop specified by args 1 and 2. In thismode the first structure minimized is that originally provided.1 Remove the loop specified by args 1 and 2 and replace it with the amino acidsequence specified in an in_filename.lsq file. Candidate loop structures will begenerated for this new loop. This file consists of a list containing codes for theamino acids; one to a line starting from the N terminus of the loop. For the 20 commonamino acids the standard 3-letter codes are used. However, the code for anyamino acid present in Maestro’s modifiable fragment tables may be given providedthat it is an alpha amino acid.MacroModel 9.7 Reference Manual 95