AMBER Archive (2006)

Subject: Re: AMBER: parameters !!??

From: Urszula Uciechowska (urszula.uciechowska_at_pharmazie.uni-halle.de)
Date: Wed Oct 25 2006 - 08:32:49 CDT

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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