[gmx-users] Two [ dihedrals ] sections in topology

Justin A. Lemkul jalemkul at vt.edu
Tue May 15 21:04:01 CEST 2012

On 5/15/12 2:53 PM, Lara Bunte wrote:
> Hi
>> Is there some reason to believe you should not have dihedrals?  That doesn't
>> make much physical sense.
> I want and have dihedrals in my topology. I don't want an additional empty dihedrals block in the topology. In my force field I gave impropers.

Please see my previous replies regarding what you're calling "empty" dihedrals. 
  There's nothing necessarily wrong with them (unless they raise an error), and 
if pdb2gmx created them then they almost certainly need to be present.  Each 
rotatable bond has a dihedral term associated with it, even if it's not 
something you thought of previously or defined explicitly in the .rtp entry.



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


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