VMD-L Mailing List

From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Fri May 22 2020 - 11:50:36 CDT

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