[gmx-users] Charmm (cgenff) Str file
jalemkul at vt.edu
Wed Mar 22 14:23:35 CET 2017
On 3/22/17 5:46 AM, RAHUL SURESH wrote:
> I have obtained stream file for an organic molecule using cgenff.parachem
> From my str file
> "RESI C:\Use 0.000 ! param penalty= 43.000 ; charge penalty=
> Here can I change the resname manually?
Yes, as long as it is consistent with the residue name in the .mol2, which
apparently was garbage to begin with (looks like a full path to a file rather
than a molecule name).
> What does the term param penalty indicate?
Start by having a look at the CGenFF literature. But in short, it's an
indicator of quality; the stream file itself has notes about what is acceptable
and what is not.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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