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

From: Fabrício Bracht <>
Date: Fri, 10 Aug 2012 09:47:02 -0300

Hi Ben. Any progress on the problem yet?
Thank you

2012/8/5 Ben Roberts <>:
> 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.
> Cheers,
> Ben
> 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
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Received on Fri Aug 10 2012 - 06:00:06 PDT
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