VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 05 2018 - 14:51:53 CST

Hi,
  Can you send me a copy of the PSF file(s) that fail to load
in psfgen (or VMD)? This may indicate a limitation or other
problem with the PSF reader in psfgen, but it's impossible to say
without a copy of the file that is giving trouble. Please gzip
any file(s) you send.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 27, 2018 at 08:11:08AM +0545, Denish Poudyal wrote:
> Dear all,
> I am working with protein(4LNX.PDB) and it has residues like T3 and
> T44(which is infact T4 molecule). I splitted the pdb into T3.PDB, T4.PDB
> and the pdb containing only proteins(4lnxprot.pdb). Running psfgen
> generated psf for 4lnxprot.pdb, but cant work for T3 & T4.pdb. So I
> converted these smaller pdbs to .mol2 and generated their psfs using
> SwissParam([1]www.swissparam.ch). But the problem is, so generated psfs
> are not being merged. It shows error "psfgen) reading structure from psf
> file T3.psf
> psfgen) error reading atoms from psf file
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.". So help
> me on generating psf using psfgen for smaller molecules or help me to
> merge so generated psfs.Â
> Thank you.
> --
> Denish Poudyal
> CDPTU, Nepal
>
> References
>
> Visible links
> 1. http://www.swissparam.ch/ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/