VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 19 2021 - 11:28:51 CDT

Thanks guys!

Best,
  John

On Fri, Jul 16, 2021 at 09:29:41PM +0000, Gumbart, JC wrote:
> 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 <[1]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 [[2]jason_smith_18_at_sfu.ca]
> Envoyé : mardi 13 juillet 2021 17:56
> À : ABEL Stephane; [3]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: [4]owner-vmd-l_at_ks.uiuc.edu <[5]owner-vmd-l_at_ks.uiuc.edu> on behalf
> of ABEL Stephane <[6]Stephane.ABEL_at_cea.fr>
> Sent: Tuesday, 13 July 2021 6:51:45 AM
> To: [7]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 ([8]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
> "
>
> References
>
> Visible links
> 1. mailto:Stephane.ABEL_at_cea.fr
> 2. mailto:jason_smith_18_at_sfu.ca
> 3. mailto:vmd-l_at_ks.uiuc.edu
> 4. mailto:owner-vmd-l_at_ks.uiuc.edu
> 5. mailto:owner-vmd-l_at_ks.uiuc.edu
> 6. mailto:Stephane.ABEL_at_cea.fr
> 7. mailto:vmd-l_at_ks.uiuc.edu
> 8. https://urldefense.com/v3/__HTTP://WWW.CHARMM-GUI.ORG__;!!DZ3fjg!tKLupJ90nzW5hae5Tx0sRDcfICoZm6iWgec9oYzYrecnHSBKUWXLPzNKR-MGcKb6zw$ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/