Benjamin Er wrote:
Hello Everybody,
I have 2 different protein chains (not a homodimer), chain C and chain F
in a PDB file.
These 2 proteins are interacting proteins close in proximity.
I would like to use energy minimization (EM) and equilibration (EQ) to
approximate the most relaxed interacting conformation between these 2
proteins.
However, after EM, these 2 chains become far apart in space. (I checked
with PyMOL using editconf for the resulting EM .gro file)
My previous EM and EQ run for a different set of 2 proteins did not have
this error.
May I please know how I can rectify this?
This sounds like a normal consequence of PBC.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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