VMD-L Mailing List

From: Sibel Cakan (sibelc_at_stu.khas.edu.tr)
Date: Wed Mar 30 2011 - 07:39:51 CDT

Dear all
I have performed a CG MD simulation of a protein which is embedded in a membrane.Now I am trying to reverse coarse-grained into all atom structure using the CG Tools plugin in VMD 1.8.7 for comparing CG simulation results with all-atom simulation.
But the reversed structure have some unusual bonds (like a triangle,etc.) .I tried to reverse initial CG structure before MD was done and this worked there are not unusual bonds or anything else.
Any suggestion would be appreciated.
Thank you
Sibel