Re: [AMBER] Metal parametrization problem!!

From: Pengfei Li <ambermailpengfei.gmail.com>
Date: Fri, 1 Aug 2014 17:42:57 -0400

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

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Received on Fri Aug 01 2014 - 15:00:03 PDT
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