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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