[gmx-users] constrained bonds

[Justin Lemkul]

On 12/2/14 1:19 PM, marzieh dehghan wrote:
> Hi every body
>
> I created covalent bond by the latest version of autodock.according to the
> tutorial of protein-ligand complex with gromacs, the result of covalent
> bond was used for MD. after energy minimization, ligand was separated from
> protein.
>
>   I would like to know how can I occur constrained bond between protein and
> ligand to keep them in the suitable distance?
>

If you need an actual bond, as in the case of a covalently bound ligand, this is 
a somewhat different case from most tutorials, which deal with the trivial case 
of noncovalent binding.  In the case of a covalently bound ligand, you need to 
introduce a new residue into the force field.

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

-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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