AMBER Archive (2004)

Subject: Re: AMBER: metal atoms in Xleap

From: Atilio Anzellotti (aanzellotti_at_mail2.vcu.edu)
Date: Fri Aug 20 2004 - 15:25:47 CDT

Dear Dr. Sponer,

  Many Thanks for the information.

Best Regards.

Atilio.
-------------------
> Dear Atilio,
> For platinum II one of the best force fields should be that
> by Jirka Kozelka,
> Elizondo-Riojas MA, Kozelka J
> J. Molec. Biol
> 314 (5): 1227-1243 DEC 14 2001
>
> this is AMBER DNA duplex simulation.
>
> May be this could help you.
>
> However, note that in general transition metal
> cations are far beyond applicability of any pairadditive
> force field. To get at least some results one
> needs to parametrise specialised force field for
> a given ligand shell of the metal.
>
> regards Jiri
>
>
> -------------------------------------------------------
> Jiri Sponer
> Professor of Biophysics
> Institute of Biophysics
> Academy of Sciences of the Czech Republic
> Kralovopolska 135
> CZ-61265 Brno
> Czech Republic
> e-mail: sponer_at_ncbr.chemi.muni.cz
> fax: 420 5412 12179
> phone: 420 5415 17133
> http://www.ibp.cz/labs/LSDNA/
> http://ncbr.chemi.muni.cz
> --------------------------------------------------------
>
>
>
> > Hello,
> >
> > As requested please find attached the leap.log file. I am working
> > specifically with Platinum.
> >
> > Many Thanks.
> >
> > Atilio.
> >
> >
> > -------------------
> > > Hi Atilio,
> > >
> > > Please send your leap.log file to the list so we can better
assess
> > the
> > > problem.
> > >
> > > Thanks,
> > >
> > > Rhonda
> > >
> > >
> > > On Thu, 19 Aug 2004, Atilio Anzellotti wrote:
> > >
> > > > Dear sir(s),
> > > >
> > > > I am trying to model some DNA-transition metal interactions,
but
> > > > xleap is not recognizing the metal atom. So far I have chosen
> > > > leaprc.gaff as a source and I used the command: mods =
> > loadamberparams
> > > > frcmod.xxx, to load a valid force field for the metal ion. But
> > when I
> > > > select the complex, xleap cannot assign the atom type nor the
> > charge
> > > > to the metal.
> > > >
> > > > I will appreciate your help on this regard, and also all the
> > > > information regarding working with metal ions in Amber that
you
> > can
> > > > provide me.
> > > >
> > > > Thanks and Best Regards.
> > > >
> > > > Atilio Anzellotti.
> > > >
> >
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> > >
> >
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>
> [ Attachment, skipping... ]
>
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