AMBER Archive (2009)

Subject: [AMBER] Topology Reorder for EVB

From: Andrea Coletta (a.coletta_at_caspur.it)
Date: Mon Dec 07 2009 - 09:58:50 CST

Hello,

I was planning to use the EVB facility in Amber9 to explore an
intramolecular proton transport.
As I've read on the manual, I need two topologies for the two diabatic
states, but I also need the atom order to be the same and I can't figure
it out how to do that.

I have two .gzmat, containing the output of QM optimization for each
state, in which the atoms' order is the same.

When I process they with antechamber to obtain the prep, the order in
the output is not the same: the proton is in a different position, in
consequence of the different topology (the hydrogen pass from a group to
another, and if I try to change manually the order, I get a wrong topology).
I've googled and found somebody who said to use a .mol2 instead of
.prep... but i can't obtain a mol2 neither with antechamber
(segmentation fault!) nor openbabel (no output)...

Somebody can help me?

Thanks

Andrea Coletta
Università degli Studi di Roma "Tor Vergata"

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber