Hi Ben. I tried to send you an email with the invitation to a shared
folder in dropbox, but the email has returned with a failure notice.
I've used the email address that is on the header of the emails you
send to the list. Can you confirm if you received the message?
Thank you
2012/8/13 Ben Roberts <ben.roberts.geek.nz>:
> 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 Tue Aug 14 2012 - 11:00:04 PDT
