[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:
>> 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
jalemkul[at]vt.edu | (540) 231-9080
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