[gmx-users] CHARMM or AMBETR forcefield for methylated glutamine and glutamic acid.

Justin Lemkul jalemkul at vt.edu
Thu Feb 7 19:48:05 CET 2019

On 2/6/19 9:38 AM, Gyorgy Hantal wrote:
> Hi,
> I think you should be able to do that if there are (and I think there
> should be) corresponding entries in the chramm/amber rtp file.

Neither AMBER nor CHARMM has methylated glutamine.

> If this sounds alien to you, try find out what is the way to generate
> topologies from a residue database (e.g. gromacs manual or tutorials).
> Hope this sounds sensible.

One could likely import parameters from N-methylacetamide for me-Gln, 
but this approach would of course have to be validated, which will 
require QM calculations for either of those force fields. That's a 
decidedly non-GROMACS issue at that point.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list