Re: [AMBER] Metal parametrization problem!!

From: Pengfei Li <ambermailpengfei.gmail.com>
Date: Mon, 4 Aug 2014 21:58:40 -0400

Hi Pedro,

Sorry for one mistake in last email. I checked the version of G09 I used, it is G09-C1.
MCPB does't support the force constant calculation using this version. I am not sure whether
MCPB supports the G09-A1 version. You can try to test it.

All the best,
Pengfei

On Aug 4, 2014, at 9:51 PM, Pengfei Li <ambermailpengfei.gmail.com> wrote:

> Hi Pedro,
>
> For the force constant part calculation, it doesn't support Gaussian 09.
> I recommended you to use Gaussian 03 to do the calculation. The support
> for G09 are considered to be added in the future.
>
> For the RESP charge calculation, if you use the Gaussian09-C.01 or more recent
> version you need to change the keyword IOp(6/33=2) to IOp(6/50=1) in the input file.
> But for G09 Revision A.01 you don't need to change the keyword in the Gaussian
> input file for RESP charge calculation.
>
> Hope it helps,
> Pengfei
>
> On Aug 4, 2014, at 9:39 PM, "Pedro A. Baldera Aguayo" <a.baldera7.gmail.com> wrote:
>
>> Hi,
>>
>> I'd like to know if MCPB supports G09 Revision A.01?
>>
>> Thanks
>>
>> Pedro
>>
>>
>> 2014-08-01 16:42 GMT-05:00 Pengfei Li <ambermailpengfei.gmail.com>:
>>
>>> Hi Pedro,
>>>
>>> MCPB may meet problems when adding the hydrogens for the water molecules.
>>>
>>> You can use tleap to add the hydrogens, it is pretty simple. Just type
>>> following command in tleap:
>>>>>>
>>> source leaprc.ff99SB
>>> mol = loadpdb Zn_L.pdb
>>> savepdb mol Zn_L_addh.pdb
>>> quit
>>>>>>
>>>
>>> But the problem is the hydrogen adding to water molecules are not well
>>> orientated. Which
>>> may cause problem in the further gaussian calculation.
>>>
>>> You can use other software to add the hydrogen first.
>>> Here is a webpage about that:
>>> http://kpwu.wordpress.com/2012/02/24/add-protons-hydrogens-to-structure/
>>> You can also use H++ website to add hydrogens:
>>> http://biophysics.cs.vt.edu/
>>> I tried to use WHAT IF and found it works well, both for protein hydrogens
>>> and water hydrogens. You can try to begin from there.
>>>
>>> For the Zinc bonding site, I think you can try to use two waters to
>>> generate the parameters.
>>> MOH is for the hydroxyl group. Since there is only one metal site connect
>>> to the 2 water oxygens,
>>> it is fine to treat them as water but not OH groups.
>>>
>>> You can check the following directory:
>>> $AMBERHOME/AmberTools/examples/mtkpp/MCPB/HHOO-1VLI/data/
>>> Where there is a MCPB example of a metal site which congaing two HIS and
>>> two water groups bonding to Zinc ion.
>>>
>>> Hope it helps, if you have other questions, please feel free to tell me.
>>>
>>> Best,
>>> Pengfei
>>>
>>> On Aug 1, 2014, at 4:13 PM, Pedro A. Baldera Aguayo <a.baldera7.gmail.com>
>>> wrote:
>>>
>>>> Hi Jason,
>>>>
>>>> Thanks again for your answer. Yes, the water molecules are part of the
>>>> metal complexes and what I did was following either MCPT or Pengfei's
>>>> tutorial, and in the 2nd step, after typing:
>>>>
>>>> MCPB -i 3PL1_OH_addHs.bcl -l 3PL1_OH_addHs.bcl.log
>>>>
>>>> I got this message
>>>>
>>>> 1 Error in watProtonate ... exiting
>>>> terminate called after throwing an instance of 'MTKpp::MTKException'
>>>> Aborted (core dumped)
>>>>
>>>> And the message in the corresponding log file is:
>>>>
>>>> ### ### ### ###
>>>> ### MTK++ Info ###
>>>> ### Function: watProtonate::run ###
>>>> ### Message: sorted water energies
>>>> ### ### ### ###
>>>>
>>>> If you have any comments about this, please let me know. Of course, I'm
>>>> still waiting for Pengfei because I think that he has already handled
>>> this
>>>> in a previous post.
>>>>
>>>> Best,
>>>>
>>>> Pedro
>>>>
>>>>
>>>> 2014-08-01 14:27 GMT-05:00 Jason Swails <jason.swails.gmail.com>:
>>>>
>>>>> On Fri, Aug 1, 2014 at 2:38 PM, Pedro A. Baldera Aguayo <
>>>>> a.baldera7.gmail.com> wrote:
>>>>>
>>>>>> Yes, I did. However, I am facing problems with the wster molecules,
>>> and I
>>>>>> do not how to deal with them.
>>>>>>
>>>>>
>>>>> ‚ÄčIf the water molecules are part of the metal complex, then I think that
>>>>> MCPB should have added the necessary hydrogens in one of the steps (or
>>> at
>>>>> least there was a step to do so, if I recall correctly).
>>>>>
>>>>> If it's just a "typical" water molecule that is part of the bulk solvent
>>>>> (or exchanges with the bulk solvent), then tleap should add those
>>>>> automatically, assuming that the water residue is named correctly.
>>>>>
>>>>> Since I'm not super familiar with MCPB, I'll let Pengfei provide more
>>>>> detailed answers if they're needed.
>>>>>
>>>>> Good luck,
>>>>> Jason
>>>>>
>>>>> --
>>>>> Jason M. Swails
>>>>> BioMaPS,
>>>>> Rutgers University
>>>>> Postdoctoral Researcher
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Pedro A. Baldera-Aguayo
>>>> National University of Engineering (UNI)
>>>> Lima - Peru
>>>> _______________________________________________
>>>> 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
>>>
>>
>>
>>
>> --
>> Pedro A. Baldera-Aguayo
>> National University of Engineering (UNI)
>> Lima - Peru
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Mon Aug 04 2014 - 19:30:02 PDT
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