Re: [AMBER] Metal parametrization problem!!

From: Pedro A. Baldera Aguayo <a.baldera7.gmail.com>
Date: Mon, 4 Aug 2014 20:39:06 -0500

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
>
> _______________________________________________
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>



-- 
Pedro A. Baldera-Aguayo
National University of Engineering (UNI)
Lima - Peru
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Received on Mon Aug 04 2014 - 19:00:02 PDT
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