From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Sat May 30 2020 - 20:33:32 CDT

Oh I see, great thanks I'll include that!

I have another question. I was under the impression that nonpolar aromatic
hydrogens are fixed to a value of +0.115, but in the CGenFF parameters only
the phenyl hydrogens are set to this charge. The indole CH hydrogens are
higher (+0.1950, +0.1960, +0.1960, and +0.2010 for the 4 CH groups going
counter-clockwise from C7 (standard indole numbering scheme)). Should these
be reset to +0.115? And/or should I exclude these from the Charge Groups
list under 'Charge Constraints' too? Couldn't seem to find a definitive
answer in the literature.

*Daniel Fellner BSc(Hons)*
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326

On Sun, 31 May 2020 at 04:49, Gumbart, JC <gumbart_at_physics.gatech.edu>
wrote:

> Oh, I didn't read very carefully - you said you did give it. But to be
> clear, you need to give it the par_all36_cgenff.prm file, which contains
> the LJ parameters. These are not in the str file produced by paramchem.
>
> Best,
> JC
> ------------------------------
> *From:* Gumbart, JC <gumbart_at_physics.gatech.edu>
> *Sent:* Saturday, May 30, 2020 12:48 PM
> *To:* Daniel Fellner <dfel694_at_aucklanduni.ac.nz>; VMD Mailing List <
> vmd-l_at_ks.uiuc.edu>
> *Subject:* Re: vmd-l: FFTK: Opt. Charges Error
>
> Hi Daniel,
>
> Did you give FFTK the cgenff parameter file? It needs the LJ parameters
> to calculate the interaction energy.
>
> Best,
> JC
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
> *Sent:* Saturday, May 30, 2020 3:58 AM
> *To:* VMD Mailing List <vmd-l_at_ks.uiuc.edu>
> *Subject:* vmd-l: FFTK: Opt. Charges Error
>
> Hi everyone,
>
> I'm using FFTK to optimise some parameters from CGenFF and after running
> and checking the water interaction files, I loaded up all the relevant data
> (including par files for both existing (blank) and cgenff parameters),
> removed the nonpolar hydrogens (including indole hydrogens which CGenFF
> assigned charges 0.1950, 0.1960, 0.1960 and 0.2010 instead of 0.1150), and
> hit Run Optimization, but I'm getting this error:
>
> can't read "ljPars(NG2O1)": no such element in array
> can't read "ljPars(NG2O1)": no such element in array
> while executing
> "lindex $ljPars($aType) 0"
> (procedure "::ForceFieldToolKit::ChargeOpt::computeIntE" line 33)
> invoked from within
> "::ForceFieldToolKit::ChargeOpt::computeIntE $i $j"
> (procedure "::ForceFieldToolKit::ChargeOpt::optCharges" line 77)
> invoked from within
> "$function $p0list"
> (procedure "construct_initial_complex" line 13)
> invoked from within
> "construct_initial_complex [lindex $args 0]"
> (procedure "::Optimize::Opt1::handle" line 89)
> invoked from within
> "$opt initsimplex [lrange $chargeInit 0 end-1] "
> (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 409)
> invoked from within
> "::ForceFieldToolKit::ChargeOpt::optimize"
> (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
> invoked from within
> "::ForceFieldToolKit::gui::coptRunOpt "
> invoked from within
> ".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
> invoked from within
> ".fftk_gui.hlf.nb.chargeopt.runOpt instate {pressed !disabled} {
> .fftk_gui.hlf.nb.chargeopt.runOpt state !pressed;
> .fftk_gui.hlf.nb.chargeopt.runOpt in..."
> (command bound to event)
>
> I recognise NG2O1 from the CGenFF stream file, but I'm not sure what
> FFTK's issue with it is.
>
>
> *Daniel Fellner BSc(Hons)*
> PhD Candidate
> School of Chemical Sciences
> University of Auckland
> Ph +64211605326
>