Protein

We consider generating the Psf file for a small protein BPTI (Bovine Pancreatic Trypsin Inhibitor). This is the standard example given in all NAMD distributions.First we get the file from protein data bank.The required file is 6pti.pdb.The required script is given below:

resetpsf

topology CHARM_top/top_all22_prot.inp

segment BPTI {
 pdb 6pti_prot.pdb
}

patch DISU BPTI:5 BPTI:55
patch DISU BPTI:14 BPTI:38
patch DISU BPTI:30 BPTI:51

alias atom ILE CD1 CD
coordpdb 6pti_prot.pdb BPTI

alias residue HOH TIP3
segment SOLV {
 auto none
 pdb 6pti_wat.pdb
}

alias atom HOH O OH2
coordpdb 6pti_wat.pdb SOLV

guesscoord

writepsf bpti.psf
writepdb bpti.pdb

The pdb file must be spilt into different segments, since psfgen require each segments to have a separate file.This is done using the grep command.

cd bpti
grep -v '^HETATM' 6PTI.pdb > 6pti_prot.pdb
grep 'HOH' 6PTI.pdb > 6pti_wat.pdb

First the protein segment is built, Disulphide links are patched between residues 5 55, 14 38, 30 51.The coordinates are read by using coordpdb command.Then the water segment is built and coordinates are read.The guesscoord is used to guess location of many atoms,hydrogen in particular.some atoms are ``poor guessed'' if needed angle and bond lengths are missing from the topologyfile.

The above things are accomplished by giving the script(bptipsf.inp) to the namd utility psfgen

psfgen < bptipsf.inp

The log file is given below:

PSFGEN from NAMD 2.5b3 for Linux-i686
reading topology file /home/gsmurthy/biosim/CHARMM_top/top_all22_prot.inp

>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<
>>>>>>>>>>>>>>>>>>>>>>> July 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu  <<<<<<<<<

Created by CHARMM version 22 1
building segment BPTI
reading residues from pdb file 6pti_protein.pdb
extracted 57 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-HN at beginning of segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
Info: segment complete.
applying patch DISU to 2 residues
applying patch DISU to 2 residues
applying patch DISU to 2 residues
aliasing residue ILE atom CD1 to CD
reading coordinates from pdb file 6pti_protein.pdb for segment BPTI
aliasing residue HOH to TIP3
building segment SOLV
disabling angle autogeneration
disabling dihedral autogeneration
reading residues from pdb file 6pti_water.pdb
extracted 0 residues from pdb file
Info: generating structure...
Info: segment complete.
aliasing residue HOH atom O to OH2
reading coordinates from pdb file 6pti_water.pdb for segment SOLV
Info: guessing coordinates for 437 atoms (4 non-hydrogen)
Warning: poorly guessed coordinates for 5 atoms (2 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1  ARG:1    BPTI
Warning: poorly guessed coordinate for atom HT2  ARG:1    BPTI
Warning: poorly guessed coordinate for atom HT3  ARG:1    BPTI
Warning: poorly guessed coordinate for atom OT1  GLY:57   BPTI
Warning: poorly guessed coordinate for atom OT2  GLY:57   BPTI
Info: writing psf file bpti.psf
total of 882 atoms
total of 896 bonds
total of 1608 angles
total of 2366 dihedrals
total of 139 impropers
Info: psf file complete.
Info: writing pdb file bpti.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.