[gmx-users] Charmm (cgenff) Str file

[Justin Lemkul]

On 3/22/17 5:46 AM, RAHUL SURESH wrote:
> I have obtained stream file for an organic molecule using cgenff.parachem
> server.
>
> From my str file
>
> "RESI C:\Use       0.000 ! param penalty=  43.000 ; charge penalty=
>  12.010"
>
> 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

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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