[gmx-users] Clayff forcefield

[Justin Lemkul]

On 8/2/17 5:20 AM, G R wrote:
>   I try to implement CLYFF in gromacs. I created ffbonded.itp,
>      ffnonbonded.itp, atomtype.atp, forcefield.doc, forcefield.itp and
>      molecule.rtp. I want  to simulate Kaolinite, and I try to use pdb2gmx to
>      create a topology. My first question is that should I create any other
>      files? second, In molecule.rtp, I just write the atom type, atom name
> and
>      charges. should I add bonds for each atom? Also, in rtp file, I don't
> know
>      what should I write as a residue?

For a system like you're dealing with, pdb2gmx is not the correct approach.  Try 
x2top with a suitable .n2t file (which you'll have to create).

-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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