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