Re: [AMBER] Side chain correction for Asp

From: David A Case <>
Date: Wed, 17 Oct 2012 12:32:16 -0400

On Wed, Oct 17, 2012, Steven Neumann wrote:
> I want to run long simulation with amber99SB*-ILDN-Q where Q states
> for the change in charges of Asp, Lys, Glu, Arg, Hip and change in
> side-chain torsion correction for Asp after refitting charges. I used
> to work with Charmm and Gmx before so I have no clue how to change the
> torsion correction for Asp (k1, k2, k3, k4, k5, k6 for N-Ca-Cb-Cg and
> for Ca-Cb-Cg-O). Could you please provide me a file in Amber99SB*-ILDN
> in which torsion corrections appear and can be changed? I know how to
> change charges which is straightforward.

Look at the frcmod.ff99SBildn file (in $AMBERHOME/dat/leap/parm). The ILDN
part is clearly marked: you should(!) be able to see where all the original
values are entered, and modify them to whatever new values you want. File
formats are given at, and you can use ParmEd
to double check your prmtop files when you are done to make sure you got what
you wanted.


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Received on Wed Oct 17 2012 - 10:00:03 PDT
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