From: jinxj (jinxj10_at_lzu.edu.cn)
Date: Sun Sep 01 2013 - 21:38:48 CDT
Dear professor:
We simulated a pentamer protein with NAMD. I am confused about that some part of the pemtamer fluctuated in and out of the box when I viewed the trajectory in VMD. Then I dealed with pbctools in vmd and failed. The command used are at below.
package require pbctools
pbc wrap -all -compound res -center com -centersel all
After this operation, all parts of the protein was centered. But there are errors in some of the structures. When I viewed the treated trajectory in VMD, the unrecognizable structure coordinates were generated.
What can I do about this problem?
Xiaojie
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