AMBER Archive (2004)

Subject: Re: AMBER: metal atoms in Xleap

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Fri Aug 20 2004 - 14:04:32 CDT

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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