AMBER Archive (2006)

Subject: Re: AMBER: parameters !!??

From: cristian obiol (c.obiol_at_qf.ub.es)
Date: Wed Oct 25 2006 - 05:29:42 CDT

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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