Re:

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Mon Mar 19 2018 - 19:13:33 CDT

Better to answer the reviewer directly: why did you use CGenFF for the ligand? Presumably because you used CHARMM36 for the protein and, therefore, it is by far the most natural choice. Mixing OPLS with C36 will be much worse.

A different question is what are the penalties provided by paramchem. If any of them are particularly bad (the file provides a couple thresholds to consider) then you may need to justify why you ignored those penalties (or just not mention them at all).

Best,
JC

> On Mar 19, 2018, at 3:54 PM, Srijita Paul <srijitap91_at_gmail.com> wrote:
>
> 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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <http://goo.gl/Q3TBQU>
> https://github.com/giacomofiorin <https://github.com/giacomofiorin>

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