Re: [AMBER] Metal parametrization problem!!

From: Pedro A. Baldera Aguayo <a.baldera7.gmail.com>
Date: Mon, 4 Aug 2014 21:46:58 -0500

Hi Pengfei,

Thanks for the advice. Right now I'm dealing with the large.bcl file. Most
of the examples provided by MCPB are for Zn; however for the

setMKRadii zn 1.1

I've been searching this value for Fe without success. Do I need to provide
this parameter by a Gaussian keyword?

Best!

Pedro


2014-08-04 20:58 GMT-05:00 Pengfei Li <ambermailpengfei.gmail.com>:

> 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
> >>>
> >>> _______________________________________________
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> >>>
> >>
> >>
> >>
> >> --
> >> 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 - 20:00:03 PDT
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