[gmx-users] Manual reparameterization for ligand topology

[Justin Lemkul]

On 8/14/19 7:29 AM, DEEPANSHU SINGLA wrote:
> I used the CGenFF program for generating the ligand topology. The GROMACS
> tutorial recommends the manual reparameterization of force field in case
> the penalty score exceeds 50. My ligand penalty scores exceed 50 and don't
> know how to change the parameters. Please help in this regard. I am
> attaching the str file of ligand generated by using the CGenFF server.

There is a CGenFF tutorial online. The 2010 JCC paper is also a complete 
theoretical background and case study/tutorial, as well. I suggest you 
start there.

-Justin

-- 
==================================================

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
http://www.thelemkullab.com

==================================================