From: ABEL Stephane (Stephane.ABEL_at_cea.fr)
Date: Tue Jul 13 2021 - 12:35:20 CDT

Thanks Jason for your response.

Unfortunately with the latest version of VMD a53 W10 64 bits I still have the psf error but not with 1.9.3 release version of VMD. So I think there is a problem with the current alpha versions of VMD for windows

Thanks

Stéphane

----------------------------------------------------------
Stéphane Abel, Ph.D., HDR
CEA Centre de Saclay
DRF/JOLIOT/I2BC-S/SB2SM/LBMS
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
________________________________________
De : Jason Smith [jason_smith_18_at_sfu.ca]
Envoyé : mardi 13 juillet 2021 17:56
À : ABEL Stephane; vmd-l_at_ks.uiuc.edu
Objet : Re: MolID error using fftk with VMD 1.94a49 on windows 10

Dear Abel,

you appear to be a few versions behind on the alpha (that's the a49 in the version number). John and Co. put a lot of great work into a more recent version. Maybe download the current alpha (or the 1.9.3 release version) and see if the problem goes away? Good luck.

Cheers,

-
Jason Smith
Post-Doctoral Fellow
Robert N. Young Lab, Simon Fraser University
8888 University Drive, Burnaby, BC, V5A-1S6
Canada

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of ABEL Stephane <Stephane.ABEL_at_cea.fr>
Sent: Tuesday, 13 July 2021 6:51:45 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: TR : MolID error using fftk with VMD 1.94a49 on windows 10

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
"