VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Fri Jul 16 2021 - 16:29:41 CDT

Hi Stéphane,

Well, I like to think that FFTK is so mature that there are no new bugs to be found, but it’s good to be humbled from time to time! In fact, you found one in the code recently added to handle lone pair particles (part of the latest iteration of CGenFF). Andrew Pang in the lab, who wrote that part, says as a quick fix, you can

>> delete the line " 0 0 !NUMLP NUMLPH" from their psf file.

And we will patch FFTK so it doesn’t happen in future versions.

Best,
JC

On Jul 13, 2021, at 1:35 PM, ABEL Stephane <Stephane.ABEL_at_cea.fr<mailto:Stephane.ABEL_at_cea.fr>> wrote:

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<mailto:jason_smith_18_at_sfu.ca>]
Envoyé : mardi 13 juillet 2021 17:56
À : ABEL Stephane; vmd-l_at_ks.uiuc.edu<mailto: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<mailto:owner-vmd-l_at_ks.uiuc.edu> <owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>> on behalf of ABEL Stephane <Stephane.ABEL_at_cea.fr<mailto:Stephane.ABEL_at_cea.fr>>
Sent: Tuesday, 13 July 2021 6:51:45 AM
To: vmd-l_at_ks.uiuc.edu<mailto: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
"