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

[bipin singh]

Thank you Dr. Justin for your reply. I am able to solve the problem by
using the -chainsep and -merge option simultaneously.




*-------------------Thanks and Regards,Bipin Singh*

On Wed, Dec 10, 2014 at 6:15 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
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