[gmx-users] dissociation of protein/peptide complex in the pdb derived from .xtc

[Justin Lemkul]

On 6/16/14, 9:05 AM, Saman Shahriyari wrote:
> dear users I have an .xtc file regarding an interacting protein/peptide
> complex. as i extract a pdb from this trajectory, i find the peptide
> separated from protein and in a position very far from it. i derived a pdb
> from .tpr file, to make sure that my starting structure is intact compared to
> the modeled structure that i used for preparing the .tpr file. i wondered
> whether the " -pbc rot+trans" and "-center" options of "trajconv" may help.
> but i still find the peptide far away from protein structure. is there any
> suggestion on how to fix this?

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

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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