[gmx-users] How to define cross-linking bonds

[Justin Lemkul]

On 3/14/17 10:13 AM, Jon Mujika wrote:
> Dear Gromacs users,
>
> I am preparing a system made of polymer chains, which are cross-linked,
> that is, there are covalent bonds between residues of different chains. I
> have managed to built the structure, including the linking. To do that, I
> used the specbond.dat file, where I specified the geometrical criteria to
> consider a link covalent bond, replacing the corresponding residues by new
> ones (with the C atoms involved in the covalent bond deprotonated). This is
> analogous to define disulphur bridges in a protein.
>
> Once the new covalent bonds are identified and the protonation state of the
> C atoms updated, I guess I need to assign the bond parameters (force
> constant and r0 value) for these new linking bonds. How should I proceed to
> add these parameters to the topology file? I would really appreciate any
> help in this issue.
>

Bonded parameters can be added to ffbonded.itp or #included as a separate .itp 
file in the topology created by pdb2gmx (since the only time it matters is when 
you get to grompp).  If you have new types for a covalent bond, you will also 
have new angles and dihedrals to add.

-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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