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

From: Fabrício Bracht <>
Date: Sun, 5 Aug 2012 11:39:03 -0300

Hi Ben. No, I did pretty much the same thing described on the MTK++
manual standard procedure. I did the same thing for parameterizing the
same active site, but instead of a water molecule I had an hydroxyl
ion. The procedure with the hydroxyl ion worked like a clock. If you
like, I can send you some of the files. Just tell me if you need
Fabrício Bracht

2012/8/5 Ben Roberts <>:
> 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?
> Cheers,
> Ben
> 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

AMBER mailing list
Received on Sun Aug 05 2012 - 08:00:02 PDT
Custom Search