Hi Fabrício,
Yes, I did. I'm not sure why it would be reporting a failure.
Cheers,
Ben
On 15/08/2012, at 5:55 AM, Fabrício Bracht wrote:
> 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 - 14:30:03 PDT
