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

[Syed Azeem]

> On 5/31/17 8:26 AM, Syed Azeem wrote:
>>> 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.
>>
>
> Sounds like a periodicity issue.  PyMOL is only telling you what's there;
> it's
> not "creating" anything :)
Hey Justin,

How do I overcome this periodicity issue?

Thanks in advance

Azeem

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