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

Valentina valentina.erastova at durham.ac.uk
Tue Jul 30 13:04:42 CEST 2013


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


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