From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Jun 22 2012 - 23:32:42 CDT

Add the line "27 1" at the beginning of your topology file (it's a weird charmm compatibility thing). Also make sure to add the line "AUTO ANGLES DIHE" somewhere in the file.

On Jun 22, 2012, at 9:13 AM, Traci Clymer wrote:

> I am trying to use psfgen to generate a psf file for bicarbonate. It creates the files but they are empty. I think the problem is with my topology file but I'm not sure exactly what it is. Any help would be greatly appreciated!
>
> This is the output I get from the TK console and I have attached my topology, pdb, and pgn files
> <BCT_VMD.pdb><bct.pgn><top_bicarb.txt>
>> Main< (VMD_files) 3 % resetpsf
> clearing structure, preserving topology and aliases
>> Main< (VMD_files) 4 % source bct.pgn
> reading topology file top_bicarb.txt
>
> building segment X
> reading residues from pdb file BCT_VMD.pdb
> extracted 1 residues from pdb file
> Info: generating structure...
> Info: segment complete.
> reading coordinates from pdb file BCT_VMD.pdb for segment X
> Warning: failed to set coordinate for atom C BCT:107 X
> Warning: failed to set coordinate for atom O3 BCT:107 X
> Warning: failed to set coordinate for atom O2 BCT:107 X
> Warning: failed to set coordinate for atom O1 BCT:107 X
> Warning: failed to set coordinate for atom H3 BCT:107 X
> Info: guessing coordinates for 0 atoms (0 non-hydrogen)
> Info: writing pdb file BCT1.pdb
> Info: pdb file complete.
> Info: writing psf file BCT1.psf
> total of 0 atoms
> total of 0 bonds
> total of 0 angles
> total of 0 dihedrals
> total of 0 impropers
> total of 0 cross-terms
> Info: psf file complete.
>> Main< (VMD_files) 5 %
>
>