[gmx-users] Standard residue of C4S shown as missing in residue topology database

[Justin Lemkul]

On 2/19/14, 11:48 PM, Libin wrote:
> Hi,
>
> I downloaded chondroitin 4 sulfate from online PDB data bank and gave it as
> input to pdb2gmx. But, it is showing error as GC4, ASG and BDP are missing
> in residue topology database. I have found that these are residue names that
> are commonly used. So, is it wise to add the residue to the rtp file? or is
> there any other option. Please advise. Also, if I need to add it to rtp
> file, from where can I get the necessary data to be added?
>

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

http://www.gromacs.org/Documentation/How-tos/Parameterization

-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 601
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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