[gmx-users] query regarding itp file

[Justin Lemkul]

On 5/19/15 10:15 AM, soumadwip ghosh wrote:
> Thanks Mark for the prompt reply. I can probably make the posre files if
> required now. But I would be relieved if someone sheds light on the first
> question that if I already have an .itp file is is necessary to make an
> entry for the atoms in the aminoacid.rtp file of the corresponding force
> field? I did not do pdb2gmx to generate the topology of the graphene

No.  The .rtp entries are only used by pdb2gmx; if you've obtained the topology 
by other means the .rtp is totally irrelevant.

> molecule since I obtained the same from PARAMCHEM and the atom types used
> for graphene are CA and HP which are consistent with some literature. Do I
> need to modify my aminoacid.rtp file or can I be assured that proper
> interactions would arise since I am using A BETTER FORCE FIELD (CHARMM 27)
> for a longer MD simulation (200ns) as per the suggestion by Justin. As far
> I am concerned the outputs of PARAMCHEM are reliable. I am confused whether
> I have provided the correct .itp file and whether the expected interaction
> would arise or not.
>

The parameters of a graphene sheet or a CNT should be very straightforward for 
an additive model.  Whether or not you'll be able to observe the desired outcome 
depends on whether or not *any* force field can capture that behavior. 
Materials like graphene and CNT have interesting electronic properties that may 
play a role here, none of which would be captured by any additive MM model.  Use 
the literature as a guide.  If anyone has attempted something similar, use that 
as inspiration.  The CHARMM force fields for nucleic acids (I would recommend 
CHARMM36 over CHARMM27) are quite good in terms of modeling subtle behavior of 
nucleic acids.  It should be about as good of a model as you'll find.  Whether 
or not the DNA-graphene interaction is described well, that I don't know.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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