VMD-L Mailing List

From: Pavan Ghatty (pavan.vmd_at_GMAIL.COM)
Date: Mon Aug 28 2006 - 16:00:42 CDT

Hello all,
I am triying to create psf files using psfgen.
My input file is

"package require psfgen
topology top_all27_prot_lipid.inp
alias residue HIS HSE
alias atom ILE CD1 CD
segment U {pdb newM1-5.pdb}
coordpdb newM1-5.pdb U
guesscoord
writepdb prot.pdb
writepsf x-plor prot.psf"
And the output I got was..

reading residues from pdb file newM1-5.pdb
extracted 170 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping cross-term C-N-CA-C-N-CA-C-N 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 cross-term C-N-CA-C-N-CA-C-N 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.
U:1
U:170
Info: segment complete.
reading coordinates from pdb file newM1-5.pdb for segment U
Warning: failed to set coordinate for atom O1 ALA:34 U
Warning: failed to set coordinate for atom O2 ALA:34 U
Warning: failed to set coordinate for atom HN1 GLY:35 U
Warning: failed to set coordinate for atom HN2 GLY:35 U
Warning: failed to set coordinate for atom HN3 GLY:35 U
Warning: failed to set coordinate for atom OT1 ALA:68 U
Warning: failed to set coordinate for atom OT2 ALA:68 U
Warning: failed to set coordinate for atom HT1 GLY:69 U
Warning: failed to set coordinate for atom HT2 GLY:69 U
Warning: failed to set coordinate for atom HT3 GLY:69 U
Warning: failed to set coordinate for atom OT1 ALA:102 U
Warning: failed to set coordinate for atom OT2 ALA:102 U
Warning: failed to set coordinate for atom HT1 GLY:103 U
Warning: failed to set coordinate for atom HT2 GLY:103 U
Warning: failed to set coordinate for atom HT3 GLY:103 U
Warning: failed to set coordinate for atom OT1 ALA:136 U
Warning: failed to set coordinate for atom OT2 ALA:136 U
Warning: failed to set coordinate for atom HT1 GLY:137 U
Warning: failed to set coordinate for atom HT2 GLY:137 U
Warning: failed to set coordinate for atom HT3 GLY:137 U
Info: guessing coordinates for 8 atoms (4 non-hydrogen)
Info: writing pdb file prot.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.
Info: writing psf file prot.psf
total of 2518 atoms
total of 2542 bonds
total of 4603 angles
total of 6649 dihedrals
total of 454 impropers
total of 168 cross-terms
Info: psf file complete.

The input pdb file had 2530 atoms. psfgen complained about 20 atoms, guessed
8 of them and ignored the remaining 12 while writing the final pdb file. The
problem as I see it is as follows. The pdbfile contains 5 strands each with
a NH3+ and COO- terminal groups which would mean the there will be 5 N
terminals and 5 C terminals. The complaints, however are on all terminal N's
and C's except the first N and the last C termini. I tried separating the
strands with a TER but no luck.
I tried both writepsf x-plor and charmm. [ I finally want x-plor psf file
for a namd run].

Any help is appreciated.

Thanks and sorry for my previous question without explanations.

Pavan.