Re:

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Mar 19 2018 - 07:58:36 CDT

I can't speak much to the specifics of OPLS/AA vs CGenFF in terms of
validation, nor can I say anything about a reviewer comment.

Maybe someone else has more experience here, but as I said before, I don't
know of any current automatic mechanism in NAMD to facilitate mixing and
matching CHARMM/OPLS due to the need for different Lennard-Jones mixing
rules. The only possible route that I can think of (and I have no idea if
this has ever been attempted before or is even recommendable), would be to
prepare a specialized PRM file that pre-mixes the parameters from
OPLS/CHARMM using NBFix statements (these pre-declare the pair parameters
and override the mixing behavior).

That's the most help I can provide.

Cheers,
BKR

On Mon, Mar 19, 2018 at 5:16 AM, Srijita Paul <srijitap91_at_gmail.com> wrote:

> 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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