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

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

Virginia Tech Department of Biochemistry
340 West Campus Dr.
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jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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