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
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Oct 29 2006 - 06:07:05 PST
