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

Justin A. Lemkul jalemkul at vt.edu
Sun Jun 27 05:30:49 CEST 2010

Moeed wrote:


> 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.


> Thanks for your attention.
> Moeed


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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