Re:

From: Srijita Paul (srijitap91_at_gmail.com)
Date: Mon Mar 19 2018 - 14:54:36 CDT

Yes I mentioned everything correctly. The reviewer's doubt is on the choice
of force field of the ligand not of the protein.
   Thank you

On 19 Mar 2018 6:39 p.m., "Giacomo Fiorin" <giacomo.fiorin_at_gmail.com> wrote:

Hello Srjita, did you write correctly that you are using the "CHARMM
*general* force field" for the protein? If so, the reviewer's comment may
be about the choice for the protein, not the ligand.

Giacomo

On Mon, Mar 19, 2018 at 8:58 AM, Brian Radak <brian.radak_at_gmail.com> wrote:

> 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?
>>>>
>>>
>>>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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