VMD-L Mailing List

From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Fri Jun 22 2012 - 13:21:35 CDT

Hi,

Try to generate new Force Fields parameters for Bicarbonate using web resources like SwissParam or ParamChem.

Regards,

Flavio

--- On Fri, 6/22/12, Traci Clymer <clymert_at_duq.edu> wrote:

> From: Traci Clymer <clymert_at_duq.edu>
> Subject: vmd-l: generating psf files for bicarbonate
> To: vmd-l_at_ks.uiuc.edu
> Date: Friday, June 22, 2012, 3:13 PM
> 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
>
> >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 %
>
>
>