[gmx-users] Protein-Ligand Covalent Bonds

[Justin Lemkul]

On 8/30/15 4:17 PM, Jordan Wolfson wrote:
> Dear Gromacs Users,
>
> Hello, I am trying to model the folding of a protein with ligands
> covalently bound to the protein. However, there is no pdb file for the
> system I am trying to run. I have been trying to figure this out for a good
> while now and have come to the conclusion that the answer lies in the
> [bonds] section of the .top file for the system. I have ran the simulation
> with the ligands before, upon using VMD I found that the ligands were just
> sitting next to the protein unbound.
>
> In the [bonds] section of the .top file, how can I specify that the ligands
> are covalently bound? I have read the gromacs manual a number of times
> looking for the answer to no avail. At one point I thought it possible that
> the answer might have to do with the function column of the bonds section
> but I have not been able to find any literature explaining what that column
> means.
>

The only "literature" is going to be the GROMACS PDF manual.

In any case, this is not simply a matter of bonds.  There are other bonded 
interactions (angles, dihedrals) and potentially 1-4 (pairs) to be dealt with. 
The simplest and best way to do this is to follow 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field - 
you have a covalent adduct to a residue.  Treat it as such.  You may have to 
reparametrize some elements (charges, atom types, internal parameters) of that 
residue as a consequence of the modification.

-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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