[gmx-users] Re. Generating topology for Tetrahydrofolate within CHARMM ff

[Justin Lemkul]

On 5/13/16 5:04 AM, zeineb SI CHAIB wrote:
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> @ Justin
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> Dear Justin,
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> Thank you very much for the website.
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> I tried to generate my topology from the website. After many problems in my input file, it finally generated the .str file with no error/warnings found but unfortunately some penalties were not good at all (> 50 and between 10 and 50)!
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> How can I fix the file?
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> 'https://cgenff.paramchem.org/initguess/#20160513/THF_zinc_4228237.str'
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You'll need to manually parametrize/refine anything that has bad penalties.

Spend some time with the CGenFF paper and tutorial:

http://dogmans.umaryland.edu/~kenno/cgenff/download.php
http://www.cecam.org/upload/files/file_1187.pdf

-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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