[gmx-users] Reg: creation of separate chains in .pdb file

[Syed Azeem]

> On 5/29/17 8:00 AM, Syed Azeem wrote:
>> Hey all,
>>
>> I simulated a protein-peptide docked complex. Post simulation, I
>> created an index file selecting only the Protein Group
>> (protein-peptide complex). Then using editconf, I created a .pdb file
>> for the same.
>>
>> When I view the prtn.pdb file, only the protein is available but not
>> the peptide. Still the prtn.pdb file has coordinates for peptide as
>> well. The pdb file also lacks a chain identifier, which was present in
>
> If you're having trouble viewing the coordinates, that's a problem with the
>
> viewer itself.  You say that the coordinates are there (as they should be)
> so
> there's no reason they can't be visualized if rendered properly.
>
>> the initial structure.
>>
>> How to overcome this?
>>
>
> Add suitable chain identifiers back into the coordinate file.

Hey Justin,

I tried adding chain identifiers naming A & B to the file. It creates
another linear peptide chain away from main complex, when I view it in
Pymol.

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