VMD-L Mailing List

From: Hamish Swanson (hamish.swanson_at_strath.ac.uk)
Date: Mon Jul 05 2021 - 12:03:23 CDT

Thank you both for your help. By refining a dihedral at a time, I have got it to work and if I meet any further problems, I will be sure to adopt the approach you suggest Harper.

Kind Regards,
Hamish
________________________________
From: Smith, Harper E. <smith.12510_at_buckeyemail.osu.edu>
Sent: 05 July 2021 17:01
To: Gumbart, JC <gumbart_at_physics.gatech.edu>; Hamish Swanson <hamish.swanson_at_strath.ac.uk>
Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: FFTK kList no such variable

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Hi Hamish,

When I had this issue, it was because I was using the .pdf/.psf pair from Molefacture. JC recommended using the following, which fixed the issue for me:

readpsf mol.psf
coordpdb.mol.pdb
regenerate angles dihedrals
writepsf temp.psf

Best,
Harper
________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Gumbart, JC <gumbart_at_physics.gatech.edu>
Sent: Monday, July 5, 2021 11:25 AM
To: Hamish Swanson <hamish.swanson_at_strath.ac.uk>
Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: FFTK kList no such variable

Hi Hamish,

Anymore, I nearly always find that errors of this nature reflect something wrong with the inputs. Try scaling back the problem to figure out which entry is causing the issue, e.g., fit just one dihedral at a time.

Best,
JC

On Jul 5, 2021, at 6:49 AM, Hamish Swanson <hamish.swanson_at_strath.ac.uk<mailto:hamish.swanson_at_strath.ac.uk>> wrote:

Hi there,

I am in the process of optimising specific dihedrals using force field toolkit using vmd version 1.9.4.

The input QM torsion are okay and the initial optimisation in the Opt. Torsions tab appears to work (e.g., all frames of Calculating relaxed MME stage are completed and terminal reads: 'Finished with coordinate file namd-temp.dcd.')

However, at this point, prior to the refinement step, I get an error message: can't read "kList": no such variable. What does this mean and how might it be remedied? Thanks.

Best Wishes,
Hamish Swanson