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AMBER Archive (2009)Subject: RE: [AMBER] problem with parametrization
From: Brothers, Michael Charles (mcbroth_at_sandia.gov)
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-----
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.
> loadamberparams glyser.frcmod
-- ignoring the error and warning.
Building topology.
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:
Could you tell me where can I find these parameters, or what parameters should I use?
Thanks in forward:
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