Re: [AMBER] Dihedral parameters for TFE with GAFF

From: case <>
Date: Fri, 21 Jan 2011 12:15:05 -0500

On Fri, Jan 21, 2011, Stephane Abel wrote:
> I am trying to build the trifluoroethanol parameters from GAFF force
> field for MD with GROMACS code.

> I can define all the bond and angle parameters. But for dihedral
> parameters, the OH C3 C3 F quadruplet is not present in the
> gaff.dat file.

You should run parmchk to get the missing parameters: Pretend you were making
an amber topology file: run antechamber, then run parmchk (see the example
in section 4.2 of the AmberTools Users' Manual). If you are lucky, parmchk
will suggest a torsion parameter for you, and you can enter that into the
gromacs files.

Of course, if the torsional barrier is important, you may want to parameterize
it by a more accurate method, as others have suggested.

...good luck...dac

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Received on Fri Jan 21 2011 - 09:30:04 PST
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