[gmx-users] (no subject)

Erik Marklund erik.marklund at kemi.uu.se
Wed Apr 5 13:23:55 CEST 2017

Dear Maria,

Are you confusing gromos and gromacs?

In the manual, under the Force fields heading: "GROMACS 2016 includes several force fields, and additional ones are available on the website. If you do not know which one to select we recommend GROMOS-96 for united-atom setups and OPLS-AA/L for all-atom parameters. That said, we describe the available options in some detail.”

(The comment about OPLS-AA/L is probably very old and in need of revision.)

Then follows subsections describing a range of supported force fields, most of which are all-atom. The phrase “united-atom” occurs only once in the manual, in the sentence quoted above. What made you think gromacs is united-atom only?

Kind regards,
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

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