From: Krishna Vkm (krishnatifr_at_gmail.com)
Date: Fri May 22 2020 - 12:40:29 CDT

Hi Stefano
   I think you have to add "EXT" next to "PSF" in the first line of your
PSF file of the ligand.
When the size of the atom name is more than 4 letters (in your case I can
see its 6 letters, *OG3C51*) VMD cannot read the file without the option
"EXT". (According to my experience).

Regards
Krishna
TIFR Mumbai

On Fri, May 22, 2020 at 10:57 PM 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
>
>