Moeed wrote:
<snip>
Q2- What I am getting is a top file but gro file processed with hdb and
rtp gives a very weird structure which has nothing to do with PE chain.
Your central problem is that your C4 unit is not aligned with any axis, so
replicating it straight along the x-axis won't work to generate the proper
geometry. Use editconf -princ to align your structure with the x-axis, then do
some simple geometry to figure out the proper value for -d to get the correct
periodic spacing.
-Justin
Thanks for your attention.
Moeed
--
========================================
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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