AMBER Archive (2006)

Subject: RE: AMBER: parameters !!??

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Oct 25 2006 - 10:53:01 CDT

Dear Urszula,

There is currently a gap in the amber tutorials where this is supposed to be
dealt with. A new tutorial is in progress that will address this issue. For
the moment though there is no link to the old tutorials that contained a
short tutorial explaining how to do this. The tutorial is still available on
my webpage however and I will probably add it to the main amber tutorials
page as a place holder why we wait for the replacement tutorial to be
finished.

See: http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/

This should give you sufficient knowledge of how to proceed. With regards to
zinc atoms binging to cysteines I suggest you check the work of Ulf Ryde who
has published several parameterizations of cysteine bound zincs - mainly to
LADH but you should be able to adapt them for your own purposes.

All the best
Ross

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|\oss Walker

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Urszula Uciechowska
> Sent: Wednesday, October 25, 2006 06:33
> To: amber_at_scripps.edu
> Subject: Re: AMBER: parameters !!??
>
>
> Hi Cristian,
>
> Thanks for your last email,I fallowed just the way you sent me,I am
> pretty new to AMber but I have no idea how can I load these
> files to the
> xleap I was trying to do that but i got some errors so
> probably it wasnt
> proper way.
>
> Thanks in advance for any help
>
> Urszula
>
> Best Regards,
>
> MSc.PhD Student
> Medicinal Chemistry Group
> University of Halle-Wittenberg
>
> ----- Original Message -----
> From: cristian obiol <c.obiol_at_qf.ub.es>
> Date: Wednesday, October 25, 2006 12:29 pm
> Subject: Re: AMBER: parameters !!??
>
> > Dear Ursula,
> > I was working with zinc containing proteins, if your metal atom has
> > a
> > tetrahedral coordination, one good alternative to model it is the
> > Pang's
> > cationic dummies atom (Protein Science, Vol 9, Issue 10 1857-
> > 1865,2000).Here it is attached the prep and parm files :
> >
> > MASS
> > DZ 0.10
> > ZD 65.380
> >
> >
> > BOND
> > DZ-ZD 540.00 0.90000
> > DZ-DZ 540.00 1.47000
> >
> >
> > ANGLE
> > DZ-ZD-DZ 35.000 109.500 JRS estimate
> > DZ-DZ-DZ 55.000 60.000 JRS estimate
> > DZ-DD-ZD 55.000 35.250 JRS estimate
> >
> >
> > DIHE
> > ZD-DZ-DZ-DZ 1 0.000 35.000 2.000
> > DZ-ZD-DZ-DZ 1 0.000 120.000 2.000
> > DZ-DZ-DZ-DZ 1 0.000 70.500 2.000
> >
> >
> > NONBON
> > ZD 3.10 1.0E-6
> > DZ 0.00 0.000
> >
> > ----And :
> >
> > 0 0 2
> >
> >
> > Zn-tetrahedral dummy
> > czd.db94
> > CZD INT 1
> > CORR OMIT DU BEG
> > 0.00000
> > 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000
> > 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000
> > 0.000 0.00000
> > 3 DUMM DU M 2 1 0 1.522 111.100 0.000
> > 0.00000 4 ZD ZD M 3 2 1 1.335 116.600
> > 180.000 0.00000
> > 5 DZ1 DZ E 4 3 2 0.900 70.500 0.000
> > 0.50000 6 DZ2 DZ E 4 3 2 0.900 70.500
> > 120.000 0.50000
> > 7 DZ3 DZ E 4 3 2 0.900 70.500 240.000
> > 0.50000 8 DZ4 DZ E 4 3 2 0.900 180.000
> > 180.000 0.50000
> >
> >
> > DONE
> > STOP
> >
> >
> > Regards,
> >
> > Cristian Obiol
> > Biological Systems Modelling and Drug Design
> > Research Group
> > University of Barcelona
> >
> >
> >
> > ------------------------------------------------------------
> > > Dear Amber users,
> > >
> > > I want to simulate a protein with the structural Zn ion. I added
> > bonds> between the Zn and four cysteine sulphur atom in xleap
> > > by typing : bond PROT.195.SG PROT.357.Zn, but I coulnd't create a
> > top> and crd files beacause i need tha parameters for this.
> > > I hope that somebody can help me in creating frcmod file.. I read
> > also> the tutorial but it didnt help me, it still doesnt
> work with me.
> > >
> > >
> > > Any suggestion would be very appreciated!!
> > >
> > > Urszula
> > >
> > > ------------------------------------------------------------------
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