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

From: Ben Roberts <>
Date: Mon, 6 Aug 2012 12:43:37 +1200

Righto. I'll have a look at the docs tonight and see if I can recall the procedure. Then I'll ask for whatever I think I need.


On 6/08/2012, at 2:39 AM, Fabrício Bracht wrote:

> 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
> anything.
> 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
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Received on Sun Aug 05 2012 - 18:00:02 PDT
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