AMBER Archive (2009)

Subject: Re: [AMBER] Topology Reorder for EVB

From: E.M. (pckboy_at_gmail.com)
Date: Mon Dec 07 2009 - 13:17:44 CST

I am just curious. What kind of software did you use to parametrize the
diabatic factors?.

regards

edu
Andrea Coletta wrote:
> 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"
>
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