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

[Justin Lemkul]

On 5/2/16 12:58 PM, zeineb SI CHAIB wrote:
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> Dear gmx users,
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> I'm working on simulating a protein with two cofactors (hem and tetrahydrofolat) and its substrate. I'm in the first stage; generating topology. I choose CHARMM27 as a force field and I'm little bit confused on how to generate tetrahydrofolate's topology.
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> I tried the online tool of SwissParam but it doesn't work, although it worked with the substrate ( an amino-acide).
> Failure message: "Unfortunately, topology and parameters were not successfully generated for THG."
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> Is there any other tools that I can use? Are they reliable? In other words: what are my options (pros and cons of each server/method?).
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https://cgenff.paramchem.org/

-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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