VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Aug 28 2006 - 16:11:11 CDT

Hi Pavan,
if you have 5 separate chains, you need to split it into 5 separate pdb
files and use a segment statement for each of them. The terminal patches
will only be applied to the very beginning and end of a segment, which
is why your internal terminii are causing problems.
Peter

Pavan Ghatty wrote:
> 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.
>