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

Saman Shahriyari samanshahriyari at yahoo.com
Mon Jun 16 15:11:04 CEST 2014

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?

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