There is actually a program designed that generates the forcefield files that are complementary to those already in ff99SB (I had the same question just a few weeks ago). You need to either own GAUSSIAN or you can get an academic license for GAMESS.
The program is linked below. The tutorials are helpful. Do realize that all parameters that need to be changed (such as whether you are using GAUSSIAN, GAMES, or PC-GAMESS) is located at the bottom in the section entitled "MAIN PROGRAM".
http://q4md-forcefieldtools.org/RED/
Best,
Michael
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of janzso.brc.hu
Sent: Wednesday, June 24, 2009 11:25 AM
To: amber.ambermd.org
Subject: [AMBER] problem with parametrization
Dear Everyone!
I am trying to create a non-standard residue with antechamber to use it in tleap. This residue is the isopeptide form of the gly-ser dipeptide, where the carbonyl group of the glycine is attached to the -OH group of the serine sidechain. I have created and parametrized this molecule following the antechamber tutorial for creating non-standard residues, I also created an frcmod file with parmchk. But when I try to build a polipeptide chain using my new residue, leap complains about missing parameters. Basically the missed parameters are at the joining points of my residue with the rest of the polipeptide.
The message goes like this (I built a tripeptide in this example after loading leaprc.gaff and leaprc.ff99SB):
> loadamberparams glyser.frcmod
Loading parameters: ./glyser.frcmod
Reading force field modification type file (frcmod) Reading title:
remark goes here
> loadamberprep glyser.prepi
Loading Prep file: ./glyser.prepi
> aa = sequence { ALA GSD ALA }
> saveamberparm aa proba.prmtop proba.inpcrd
Checking Unit.
ERROR: The unperturbed charge of the unit: -0.107460 is not integral.
WARNING: The unperturbed charge of the unit: -0.107460 is not zero.
-- ignoring the error and warning.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: C - n Could not find bond parameter for: c - N Building angle parameters.
Could not find angle parameter: O - C - n Could not find angle parameter: C - n - hn Could not find angle parameter: C - n - c3 Could not find angle parameter: CT - C - n Could not find angle parameter: o - c - N Could not find angle parameter: c - N - H Could not find angle parameter: c - N - CT Could not find angle parameter: c3 - c - N Building proper torsion parameters.
** No torsion terms for O-C-n-hn
** No torsion terms for O-C-n-c3
** No torsion terms for CT-C-n-hn
** No torsion terms for CT-C-n-c3
** No torsion terms for o-c-N-H
** No torsion terms for o-c-N-CT
** No torsion terms for c3-c-N-H
** No torsion terms for c3-c-N-CT
Building improper torsion parameters.
old PREP-specified impropers:
<GSD 2>: C3 O2 C4 O3
<GSD 2>: +M C6 C7 O4
total 5 improper torsions applied
2 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved."
Since I want to use the force field ff99SB for my calculations, and the isopeptide residue was parametrized using gaff the missing parameters are aviable at both force field, but not recognized because of the capitalization. I figured I can modify the frcmod file to have leap handle these angles and bonds and dihedrals, but I could not find some of the dihedral parameters, neither in parm99.dat or gaff.dat:
O-C-n-c3
CT-C-n-hn
CT-C-n-c3
o-c-N-H
o-c-N-CT
c3-c-N-H
Could you tell me where can I find these parameters, or what parameters should I use?
Thanks in forward:
Gabor Janzso
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Received on Mon Jul 06 2009 - 11:09:43 PDT
