MMTSB
Tool Set Documentation

complete.pl

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Usage

usage:   complete.pl [options] [PDBfile]
options: [-hsd list] [-hse list] [-param 19|22|27] [-blocked]
         [-log file] [-cmd file]
         [-nosicho]
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Description

This script attempts to rebuild a complete all-atom protein structure from given incomplete atomic coordinates in PDB format. If only C-alpha atoms are present, a backbone is reconstructed first, missing side chains are then added either with the MMTSB rebuilding procedure (rebuild.pl) if C-beta atoms are available or by using SCWRL if no other atoms are available beyond the backbone. SCWRL is not part of the MMTSB Tool Set and needs to be installed separately for this functionality.
Finally, CHARMM is used to add missing hydrogen atoms and/or missing atoms at the terminal residues. The accuracy of the rebuilt structures depends on the available coordinates in the input file. If only C-alpha coordinates are given some of the side chain atom positions may be significantly different from experimental structures. The rebuilt structures should be free of severe steric clashes but will likely contain a number of quite unfavorable interactions that should be relaxed carefully before attempting further force-field based all-atom modeling. It is not possible to rebuild complete residues with this utility.

The script expects a PDB file as command line argument or from standard input. The CHARMM parameter set is selected with -param (19 or 22). If CHARMM19 is selected only missing polar hydrogens are generated, with CHARMM22 all missing hydrogens are added to the structure. The options -hsd and -hse, are available to specifiy the protonation site of single-protonated histidine residues. Both of these options are used with a list of residues separated by colons. The protein is terminated with neutral blocking groups if the option -blocked is given.
The output is written to standard output and may be redirected to a desired file name.
CHARMM output and commands sent to CHARMM can be saved to files with -log and -cmd, respectively.

Options

-help 
usage information
-hsd list 
protonates the delta position for histidine according to the given list
-hse list 
protonates the epsilon position for histidine according to the given list
-param 19|22|27 
generate a structure with naming according to the specified CHARMM force field
-blocked 
generate blocked termini
-log file 
write a logfile
-cmd file 
write out a CHARMM input file
-nosicho 
do not use SICHO model to rebuild from C-beta

Examples

complete.pl 1vii.exp.caonly.pdb
rebuilds a complete protein structure from C-alpha coordinates

ATOM      1  N   MET     1       0.774  -7.875  -4.381  1.00  0.00          
ATOM      2  HT1 MET     1      -0.029  -7.328  -4.751  1.00  0.00          
ATOM      3  HT2 MET     1       1.233  -8.387  -5.161  1.00  0.00          
ATOM      4  HT3 MET     1       1.460  -7.229  -3.940  1.00  0.00          
ATOM      5  CA  MET     1       0.292  -8.839  -3.377  1.00  0.00          
ATOM      6  HA  MET     1      -0.416  -9.495  -3.861  1.00  0.00          
ATOM      7  CB  MET     1       1.460  -9.643  -2.802  1.00  0.00          
ATOM      8  HB1 MET     1       1.080 -10.264  -1.964  1.00  0.00          
ATOM      9  HB2 MET     1       2.216  -8.931  -2.409  1.00  0.00          
ATOM     10  CG  MET     1       2.139 -10.558  -3.808  1.00  0.00          

...


complete.pl -param 19 1vii.exp.noh.pdb
adds missing polar hydrogen atoms to a structure without hydrogen atoms

ATOM      1  HT1 MET     1       0.597 -10.898  -3.480  1.00  0.00          
ATOM      2  HT2 MET     1       1.843 -10.053  -2.694  1.00  0.00          
ATOM      3  N   MET     1       1.177 -10.035  -3.493  1.00  0.00          
ATOM      4  HT3 MET     1       1.709  -9.988  -4.386  1.00  0.00          
ATOM      5  CA  MET     1       0.292  -8.839  -3.377  1.00  0.00          
ATOM      6  CB  MET     1      -0.674  -8.793  -4.565  1.00  0.00          
ATOM      7  CG  MET     1      -0.091  -7.889  -5.657  1.00  0.00          
ATOM      8  SD  MET     1      -0.153  -8.747  -7.255  1.00  0.00          
ATOM      9  CE  MET     1      -0.971  -7.432  -8.193  1.00  0.00          
ATOM     10  C   MET     1      -0.488  -8.912  -2.063  1.00  0.00          

...