[gmx-users] (no subject)

Mark Abraham mark.j.abraham at gmail.com
Wed Apr 5 12:14:44 CEST 2017


On Wed, Apr 5, 2017 at 12:00 PM maria khan <mariabiochemist1 at gmail.com>

> 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

All the MD packages *can* deploy united-atom force fields. To my knowledge,
none of them require or prohibit it. :-)

> 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.

There's introductory level guidance available here
http://www.gromacs.org/Documentation/How-tos/Parameterization but you are
warned there that this is not a topic suitable for a beginner. At the very
least, use one of the several different packages that provide automated
force-field-specific parameterization of e.g. ligand molecules, having
planned how you will assess the quality of the parameterization before
attempting to use it to solve a problem whose answer you do not know.


> Thank you.
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