[gmx-users] pdb2gmx and specbond with arbitrary ligand

[Justin Lemkul]

On 3/11/15 1:08 PM, Leandro Bortot wrote:
> Dear users,
>
>       I want to simulate some ligands covalently bonded to a protein, i.e.
> covalent inhibitors. I've searched the list and found similar issues, but
> mainly with heme in forcefields in which it is already supported. I use the
> AMBER99SB-ILDN forcefield and I can simulate the non covalent complexes
> with no problems using GAFF.
>
>       I suppose I can just put both the ligand and the protein under the
> same [moleculetype] specification in a .itp file and manually add the bonds
> in this topology. It seems that I only need a script to renumber the atoms
> to achieve this. However, I think pdb2gmx and specbond.dat may already be
> able to do this. The problem is: How can pdb2gmx understand my arbitrary
> ligand? Is adding my ligand to a local copy of
> amber99sb-ildn/aminoacids.rtp the only way?
>
>       What would be the best way to do that?
>

Yes, the .rtp approach is the most reliable way to do this.  Follow all the 
steps in 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field 
and add an entry in specbond.dat (format explained in 
http://www.gromacs.org/Documentation/File_Formats/specbond.dat)

-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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