VMD-L Mailing List

From: ABEL Stephane (Stephane.ABEL_at_cea.fr)
Date: Tue Jul 13 2021 - 08:51:45 CDT

Dear all,

I am trying to use fftk with the above mentioned version of VMD for outputting the optimized structure of my molecule obtained with gaussian 16

I provided

- the psf file obtained from CHARMM-GUI (step1_pdbreader.psf)
- The original pdb file (step1_pdbreader.pdb)
- The completed log file of GAUSSIAN16
- and the name of a PDB file to be output

When I hit the button "load QM ouput file" I obtain the following error "psf file parsing error" and when I press the "Write the optimized structure in the PDB file " the following error "expected integer but got ""Not valid molecule id in atomselect's 'molId'".

My step1_pdbreader.psf has the following header "

PSF EXT CMAP CHEQ XPLOR

         3 !NTITLE
* GENERATED BY CHARMM-GUI (http://WWW.CHARMM-GUI.ORG) V3.5 ON JUL, 13. 2021. JOB
* READ PDB, MANIPULATE STRUCTURE IF NEEDED, AND GENERATE TOPOLOGY FILE
* DATE: 7/13/21 4:30:36 CREATED BY USER: apache

        92 !NATOM
         1 ATOM 1320 TA1 O01 OG311 -0.634000 15.9994 0 0.00000 -0.301140E-02
         2 ATOM 1320 TA1 H02 HGP1 0.419000 1.00800 0 0.00000 -0.301140E-02

...

And the mol id in the main VMD gui is 2.

Could you help me to resolve this problem?

Thanks in advance

Stéphane
"