Re: [AMBER] Problems parameterizing water/ZN active site with MKT++

From: Ben Roberts <>
Date: Sun, 5 Aug 2012 17:19:53 +1200

Hi Fabrício,

Is it exactly 0 on the Zn? That does sound very suspicious. Unfortunately, the MTK++ steps are a fairly complicated procedure. Did you deviate from the standard procedure for the latter part of the MTK++ parameterisation in any way?


On 1/08/2012, at 7:36 AM, Fabrício Bracht wrote:

> Hello. After a long discussion on the parameterization of an active
> site containing zinc and a hydroxyl molecule
> (, I've started
> parameterization of the same active site, but this time with the water
> molecule instead of a hydroxyl bound to zinc. Everything seems to go
> ok, including gaussian calculations, but once I get to the creation of
> the xml files and after that, to the creation of the prep file, I see
> that the charge distribution is nothing like I would expect. The
> procedure places 0 charge on the zinc atom, 0 charge on the oxygen
> (water) atom and very small charges on the water hydrogen atoms.
> Furthermore, I've checked with the ZAFF xml files distributed with the
> original paper, and the charges are very different than the ones they
> got. The charges are very different than the ones on the ESP fit in
> the gaussian output file. Could it be something with the espgen or
> respgen routines as written in the file?
> The ESP CHARGES calculated by gaussian are : (O, H and H are the atoms
> that form the water molecule).
> Zn 0.85630372D+00
> O -0.94007825D+00
> H 0.50049376D+00
> H 0.41322947D+00
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Sat Aug 04 2012 - 22:30:02 PDT
Custom Search