VMD-L Mailing List

From: mariano spivak (mariano_at_ks.uiuc.edu)
Date: Fri Mar 29 2019 - 09:17:25 CDT

Well, the only case of nonbonded atoms in solution I can think of is the
monoatomic ions. I have not tested those myself but it might require some
adjustment in the code.
Regarding using your own Gaussian input files, you can try that, but I
would compare your results with the standard implementation before using
the charges obtained.

Mariano Spivak, Ph.D.

Theoretical and Computational Biophysics Group

Beckman Institute, University of Illinois.

mariano_at_ks.uiuc.edu

mspivak_at_illinois.edu

On Fri, Mar 29, 2019 at 12:48 AM McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> One more question on this topic. I have a crystal structure of our
> copper complex, which includes water positions on the copper atom. There
> are two waters, one in the equatorial position and one in the axial
> position. Can I create my own Gaussian Input with these two waters in
> those positions for the copper interaction part of the FFTK process and
> then use that log file, but let FFTK set up the other atom water
> interactions and use those log files? Or does FFTK include something
> specific in the Gaussian Input Files which I would miss my creating my own?
>
> *Kelly L. McGuire*
>
> *PhD Candidate*
>
> *Biophysics*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> McGuire, Kelly <mcg05004_at_byui.edu>
> *Sent:* Thursday, March 28, 2019 2:30 PM
> *To:* mariano spivak
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: FFTK Water Interaction
>
> 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> 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*
>
>
>