[gmx-users] Replicating monomer units-problem with geometry of connecting atoms

[Justin A. Lemkul]

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
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-- 
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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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