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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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