Re: [AMBER] AMBER-cis-trans conversion

From: Jason Swails <>
Date: Tue, 21 Jan 2014 11:13:24 -0500

On Tue, Jan 21, 2014 at 10:19 AM, Gözde YALÇIN <>wrote:

> I did minimization with this molecule:
> N-c3-c2-c2-c3-N
> After 1000 steps of minimization, the trans sp2 carbons(c2) convert to cis
> conformation. I couldn' t understand what can be responsible for this
> situation? Where I did a mistake?Can you help me to solve this
> problem.Thanks for your relevancy...

The simulation engines do not know anything about chemistry. The behavior
is governed entirely by the force field. Since this molecule is highly
non-polar (and it seems like there may be dangling bonds from the terminal
nitrogen atoms, unless there are extra hydrogens you did not mention), the
interactions will likely be dominated by the torsion terms and the van der
Waals interactions.

If unexpected interconversions occur (between cis-trans, for instance),
then that likely means that some of the torsion parameters are not correct.
 Gaff is good when it comes to parametrizing simple organic compounds, but
it is far from perfect and users should be wary of potentially unexpected
behavior like this. It seems like you have to modify some of the torsion
parameters (probably the h-c2-c2-h and the c3-c2-c2-c3 torsion parameters,
for instance) to make sure this does not happen.

Often, these parameters are fit to an equivalent scan using quantum
mechanical energies.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Jan 21 2014 - 08:30:02 PST
Custom Search