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

[Justin Lemkul]

On 6/1/17 4:30 AM, Syed Azeem wrote:
>> 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?
> 

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

If I had a nickel for every time I've posted that link...

-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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