VMD-L Mailing List
From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Sun May 31 2020 - 15:20:52 CDT
- Next message: Aashish Bhatt: "NAMD energy plugin reference"
- Previous message: Daniel Fellner: "Re: FFTK: Opt. Charges Error"
- In reply to: Daniel Fellner: "Re: FFTK: Opt. Charges Error"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
If the penalties are low and nothing looks unusual, we usually trust the CGenFF parameters. The less you have to optimize the better!
Best,
JC
________________________________
From: Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
Sent: Saturday, May 30, 2020 9:33 PM
To: Gumbart, JC <gumbart_at_physics.gatech.edu>
Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: FFTK: Opt. Charges Error
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<mailto: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<mailto:gumbart_at_physics.gatech.edu>>
Sent: Saturday, May 30, 2020 12:48 PM
To: Daniel Fellner <dfel694_at_aucklanduni.ac.nz<mailto:dfel694_at_aucklanduni.ac.nz>>; VMD Mailing List <vmd-l_at_ks.uiuc.edu<mailto: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<mailto:owner-vmd-l_at_ks.uiuc.edu> <owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>> on behalf of Daniel Fellner <dfel694_at_aucklanduni.ac.nz<mailto:dfel694_at_aucklanduni.ac.nz>>
Sent: Saturday, May 30, 2020 3:58 AM
To: VMD Mailing List <vmd-l_at_ks.uiuc.edu<mailto: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
- Next message: Aashish Bhatt: "NAMD energy plugin reference"
- Previous message: Daniel Fellner: "Re: FFTK: Opt. Charges Error"
- In reply to: Daniel Fellner: "Re: FFTK: Opt. Charges Error"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]