Re: [AMBER] How to modify the LENNARD_JONES_BCOEF in amber topology

From: Pengfei Li <>
Date: Sat, 7 May 2016 22:55:58 -0400

Dear Anu,

There are some commands in ParmEd about modifying the LJ parameters: e.g. “changeLJPair”, “changeLJSingleType”, and “addLJType” (you can check the AMBER manual for details). They may be helpful for your work.

Kind regards,

> On May 7, 2016, at 11:52 AM, anu chandra <> wrote:
> Dear Amber users,
> I am trying to use a modified parameter set from the literature for
> simulation, where the B coefficient of LJ potential the one atom type ( for
> e.g. atom type Z) is set as zero. In oder to implement this the amber
> topology, I have to modify the LENNARD_JONES_BCOEF values to zero for each
> pair of atom type, where atom type D in involved in the pair. Is there an
> build script in Amber that can help me to do such modification in the
> topology file?
> Many thanks in advance
> Anu
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Received on Sat May 07 2016 - 20:00:04 PDT
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