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

Justin Lemkul jalemkul at vt.edu
Tue Jul 30 13:18:55 CEST 2013



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
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University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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