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

Date: Sun, 08 May 2016 13:12:28 +0000

I think that with the current commands in Parmed it is impossible to modify Aij or Bij separately.
All commands act on rij and eij and therefore they modify the two parameters.
I believe that new commands must be introduced that allow this interesting action.


De: Pengfei Li []
Enviado: domingo, 08 de mayo de 2016 4:55
Para: AMBER Mailing List
Asunto: Re: [AMBER] How to modify the LENNARD_JONES_BCOEF in amber topology

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
> _______________________________________________
> AMBER mailing list

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Received on Sun May 08 2016 - 06:30:03 PDT
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