[gmx-users] Regarding the generation of intermolecule disulphide bond between two monomer subunits

[Justin Lemkul]

On 12/10/14 7:29 AM, bipin singh wrote:
> Hi all,
>
> I want to generate a disulphide bond between two cysteine residues of two
> monomers of a protein, to create a dimer protein. But, it is not happening
> while running the pdb2gmx, because there is TER record at the end of one
> monomer subunit pdb file. However, using the -chainsep option and defining
> the two monomers as a single molecule generate the disulphide bond but
> cause the formation of peptide bond between the two terminal ends of
> monomer chains.
> Please let me know, if there is any other way to make intermolecule
> disulphide bond, without linking the two monomers ends with peptide bond.
>

Proper use of -chainsep and -merge is all it takes to get this to work, but you 
haven't shown us what you've actually done.  Provide exact commands and relevant 
output, and we can suggest something.  But this can certainly be done with those 
two options.

-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

==================================================