Re:

From: Srijita Paul (srijitap91_at_gmail.com)
Date: Mon Mar 19 2018 - 04:16:13 CDT

Actually I have already used cgenff for both the peptide and ligand. But I
got a question from reviewer that why I am using cgenff why not other force
field. So I want to test the molecule with other force field like opls-aa.
So I thought to keep the force field of the peptide fix and vary the ff of
the ligand to check it's ff validation. Is it a right way to check it or I
can use opls-aa for both the peptide and ligand to check it?
               Thank you
Srijita Paul
IIT GUWAHATI

On 19 Mar 2018 1:57 a.m., "Brian Radak" <brian.radak_at_gmail.com> wrote:

> I don't believe that you can automatically mix arithmetic and geometric
> mixing rules (or at least I don't know of any mechanism that NAMD has with
> which to do this). My guess would be that you would have to create a
> specialized prm file that implements appropriate NBFixes for either the
> CHARMM or OPLS types.
>
> I have never heard of mixing these two force fields before - is there a
> specific reason you are not using CGenFF for the ligand? Presumably that is
> the most "literature friendly" approach.
>
> HTH,
> BKR
>
> On Fri, Mar 16, 2018 at 3:14 PM, Srijita Paul <srijitap91_at_gmail.com>
> wrote:
>
>> Hi,
>> I am trying to run a simulation where I want to use charm general force
>> field for protein and opls-aa force field for the ligand. I have saved the
>> opls-aa parameter in charm format in .prm file. But after running the
>> simulation I am getting such type of error for all the atoms of the ligand
>> and simulation failed.
>>
>> 0:463(1165) atom 648 found 0 exclusions but expected 5
>>
>> In my configuration file I also tried the command
>> "vdwGeometricSigma yes" and got the same error.
>> Can I use charm and opls-aa force field together in a same simulation. If
>> yes why this error is comming and what should I do for it?
>>
>
>

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