VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Mar 28 2019 - 15:30:56 CDT

Mariano,

  You were correct. Explicit bonds are required and need to specified in the PSF. This corrected the problem. Out of curiosity, are nonbonded atoms (no specific scenario) always a problem with FFTK?

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: mariano spivak <marspivak_at_gmail.com>
Sent: Thursday, March 28, 2019 8:19 AM
To: McGuire, Kelly
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: FFTK Water Interaction

Kelly,

Based on the error you report, the issue you experience is related to the bonds defined for the copper atoms (if any) in the psf file.
fftk is trying to generate a zmatrix around the copper to orient the corresponding water molecules, but it does not found any bonds to set a frame of reference for the zmatrix.

Can you check the psf for bonds with the copper atom? For example, if this is a coordination complex, you might need to add explicitly the bonds to the copper atom.

If you still have problems, you could send me the files (psf, pdb, par/str) and I could take a look.

Best

On Thu, Mar 28, 2019 at 12:30 AM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:
I am running into an error in the water interaction FFTK step. I have atom type that is not in the CGENFF parameters, it is copper. I have defined my own parameters based on copper CHARMM parameters from literature. FFTK identifies my copper atom as an Acceptor atom, but can't write a Gaussian Input File for it. The Gaussian Input File, CAI-ACC-Cu.gau, is blank. It correctly writes Gaussian Input Files for my other Acceptor and Donor atoms without problems. What is the workaround at this FFTK step for new atoms that need to be Acceptor atoms? I am using VMD 1.9.4a12. I believe the error is talking about the copper atom. The error says:

atomselect: cannot parse selection text: index
atomselect: cannot parse selection text: index
    while executing
"atomselect top "index $bInd""
    (procedure "::ForceFieldToolKit::GenZMatrix::writeZmat" line 167)
    invoked from within
"::ForceFieldToolKit::GenZMatrix::writeZmat $acceptorAtom acceptor $Gnames $outfile"
    (procedure "::ForceFieldToolKit::GenZMatrix::genZmatrix" line 89)
    invoked from within
"::ForceFieldToolKit::GenZMatrix::genZmatrix"
    invoked from within
".fftk_gui.hlf.nb.genzmat.run.generate invoke "
    invoked from within
".fftk_gui.hlf.nb.genzmat.run.generate instate {pressed !disabled} { .fftk_gui.hlf.nb.genzmat.run.generate state !pressed; .fftk_gui.hlf.nb.genzmat.run..."
    (command bound to event)

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602