[gmx-users] (no subject)

Vytautas Rakeviius vytautas1987 at yahoo.com
Wed Apr 5 12:13:57 CEST 2017

You can use acpype to prepare ligands for MD run.

    On Wednesday, April 5, 2017 1:01 PM, maria khan <mariabiochemist1 at gmail.com> wrote:

 Dear Erik..

I have studied the manuals of gromacs and from that i came to know that
gromacs use united atom ff thats why i asked and in manuals many things has
been explained by quantum basis,,which is not understandable for me.

How can i find ff parameters for my ligand of interest?? also if
ff parameters are not in published form then it means i will not be able to
use that ligand for MD run?? My ligand of interest is alkaloid. and i dont
know how can i make the parameters for it.

Thank you.
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