[gmx-users] Protein-Ligand Covalent Bonds

Jordan Wolfson jordan.wolfson at stonybrook.edu
Sun Aug 30 23:04:48 CEST 2015

Dear Dr. Lemkul,

Thank you for your input I will try out your recommendation.


Jordan Wolfson

On Sunday, August 30, 2015, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ==================================================
> 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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