[AMBER] RE : Dihedral parameters for TFE with GAFF

From: ABEL Stephane 175950 <Stephane.ABEL.cea.fr>
Date: Fri, 21 Jan 2011 18:21:52 +0100

Thank you Dr Case

Since I have never used AMBER. I will try your suggestion I hope it will work ! if not i will the others suggestions.


------------------------------
Stéphane Abel, PhD
CEA Saclay
DSV/IBITEC-S/SB2SM & CNRS URA2096
91191 Saclay, FRANCE
URL: http://www.st-abel.com
------------------------------



-------- Message d'origine--------
De: case [mailto:case.biomaps.rutgers.edu]
Date: ven. 21/01/2011 18:15
À: AMBER Mailing List
Objet : Re: [AMBER] Dihedral parameters for TFE with GAFF
 
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 - 09:30:06 PST
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