Hi Fabrício,
Do you think you could send me your BCL scripts, input PDB file (cleaned up and ready for MTK++), and Gaussian outputs? Or, if they're too big to email, could you put them on a web server so I can download them?
Cheers,
Ben
On 12/08/2012, at 9:48 PM, Ben Roberts wrote:
> 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
>>>>>>
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Received on Mon Aug 13 2012 - 01:30:03 PDT
