VMD-L Mailing List

From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Sun May 24 2020 - 05:51:55 CDT

Josh, thanks for your hint, that actually worked.

Stefano

Il giorno ven 22 mag 2020 alle ore 20:16 Josh Vermaas <
joshua.vermaas_at_gmail.com> ha scritto:

> 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
>>
>> 

-- 
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