[gmx-users] generating user-defined topologies for surfaces

[Justin Lemkul]

On 7/30/13 7:04 AM, Valentina wrote:
> Hello,
>
> I have a strange question with regard to set up of a FF for pdb2gmx for
> inorganic surfaces (or dendrimers).
>
> So previously I used ClayFF (i.e. non-bonded FF) and written input for
> pdb2gmx - no problem there. Now I want to use the bonded FF. So I have a
> unitcell, a residue in what gromacs knows. In molecule.rtp I know that the
> bonds between residue before (say west) is '-' and residue after (east) is
> '+', but what with the bonds on other sides, like north and south? Is it
> even doable?
>
> Dendrimers are sort of same thing - they are connected in more than 2
> directions...
>

Nonlinear bonds are generated using specbond.dat.  See the manual and wiki page 
for format and usage details.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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