VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Fri May 22 2020 - 13:16:15 CDT

Have you tried adding the NAMD tag to the psf? That switches the reader to
one delimited by spaces rather than one demarcated by columns, which is the
default.
Josh

On Fri, May 22, 2020, 11:27 AM Stefano Guglielmo <stefano.guglielmo_at_unito.it>
wrote:

> Dear all,
> I have generated psf and pdb files for a small ligand through charmm-gui,
> but when I try to merge structures of ligand and protein vmd (v. 1.9.3)
> seems unable to parse psf file:
> "psfplugin) Detected a Charmm PSF file
> psfplugin) Detected a Charmm PSF EXTEnded file
> Info) Using plugin psf for structure file
> /home/sguglielmo2/pgp_cs/glabra_param/ligandrm.psf
> psfplugin) Failed to parse atom line in PSF file:
> psfplugin) ' 1 GLAB 1 GLAB O1 OG3C51
> -0.246000 15.9994 0 0.00000 -0.301140E-02
> '
> couldn't read atom 0
> ERROR) molecule_structure: Unable to read structure for molecule 41
> ERROR) molecule_structure: severe error indicated by plugin aborting
> loading of molecule 41"
>
> Is there any solution?
>
> Thanks in advance
> Stefano
>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707178
>
>