The parametrization goes ok. I get no errors. But as far as in protein Zn is not an ion and it is bound to four surrounding amino acids then of course when I parametrize zinc as ion it losts binding to amino acids and the structure starts to become corrupted. So I think that I definitely just need to fix ainc atom and these four amino acids. This part of the structure should be fixed, probably even more amino acids because they are far from the binding site, but can innfluence the whole geometry and the binding site. Can I use it with parameters as below? Probably I should use just the part of the protein around the binding site and fix everything else?
Best regards,
Andrew
2rf5
$cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 2500000, dt = 0.002,
ntpr = 100, ntwx = 5000, ntwr = 1000
/
Keep protein fixed with weak restraints
10.0
RES 131, 134, 139, 142, 208
END
END
13.01.10, 09:47, "Ross Walker" <ross.rosswalker.co.uk>:
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Jan 18 2010 - 02:00:02 PST
