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

From: Ben Roberts <ben.roberts.geek.nz>
Date: Sun, 12 Aug 2012 21:48:08 +1200

Hi Fabrício,

No, I've been a bit busy the last week. I'll try to look into it shortly, maybe tomorrow evening.

Cheers,
Ben

On 11/08/2012, at 12:47 AM, Fabrício Bracht wrote:

> Hi Ben. Any progress on the problem yet?
> Thank you
> Fabrício
>
> 2012/8/5 Ben Roberts <ben.roberts.geek.nz>:
>> 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 <ben.roberts.geek.nz>:
>>>> 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
>>>>> (http://archive.ambermd.org/201205/0452.html), 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 getcharges.sh 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.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> --
>> For greater security, I support S/MIME encryption.
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

-- 
For greater security, I support S/MIME encryption.





_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


Received on Sun Aug 12 2012 - 03:00:02 PDT
Custom Search