Hi Andrew,
If you think the zinc is purely structural and not involved in the actual
binding site then you can just model it as a 2+ ion. Put TER cards around it
in the pdb. Call it something like residue name ZNS (for structural Zinc)
and give it atom name ZN.
Then fire up leap and do:
edit ZNS
This will create a new unit called ZNS.
Draw in a single new atom and then highlight and edit it.
Set the charge to +2, the name and type to ZN.
Then
savemol2 ZNS ZNS.mol2
Quit Leap.
Create an frcmod file with the contents:
Zinc 2+ Params
MASS
Zn 65.38
BOND
ANGL
DIHE
NONB
Zn 1.85 0.06
Finally you can fire up leap:
source leaprc.ff99SB
ZNS = loadmol2 ZNS.mol2
loadamberparams frcmod
foo = loadpdb foo.pdb
And your zinc should be recognized.
The only other thing you might have to do is make sure the protonation state
(HIS/HID/HIP, CYS/CYX etc) is correct for the residues surrounding the zinc
so you don't get H's added very close to the zinc.
Good luck,
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Andrew Voronkov
> Sent: Wednesday, January 13, 2010 2:11 AM
> To: AMBER Mailing List
> Subject: [AMBER] How to avoid Zn parametrization?
>
> Dear Amber users,
> I have a protein which has Zn atom, bound directly to four amino acids
> (Tankyrase PARP domain, 2rf5 code in PDB bank).
> I need to test the results of docking of small ligands by MD run by
> evaluation of the stability of complexes. The binding site is far from
> Zn atom. For now I have no time to make parametrization for Zn atom as
> far as it seems to be rather advanced and time consuming. What options
> do I have?
> For example I haven't included Zinc in docking site while performing
> docking. Can I maybe make CAP molecular dynamics only for the binding
> site of the ligand.
> Probably parametrize zinc as ion, or just cut out Zn atom and fix all
> Zn-surrounding amino acids as in the X-ray structure?
>
>
> Best regards,
> Andrew
>
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Received on Wed Jan 13 2010 - 10:00:06 PST
