VMD-L Mailing List

From: mariano spivak (mariano_at_ks.uiuc.edu)
Date: Thu Mar 28 2019 - 09:25:13 CDT

Sorry for the extra noise, I replied from the wrong email adress.

Mariano Spivak, Ph.D.

Theoretical and Computational Biophysics Group

Beckman Institute, University of Illinois.

mariano_at_ks.uiuc.edu

mspivak_at_illinois.edu

On Thu, Mar 28, 2019 at 9:19 AM mariano spivak <marspivak_at_gmail.com> wrote:

> 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*
>>
>>
>>