Dear Andrew,
Your Zinc atom is bound to amino-acids. Consequently, treating Zinc as
a +2 ion is quite simple but might not lead to realistic conclusions.
Deriving the charge value of a metal embedded in a bio-inorganic
complex results in a quite important decrease of the charge value in
comparison to that of the corresponding isolated ion.
If you use a 'too large' charge value for your metal embedded in a
bio-inorganic complex and/or if you constrain your system (using the
metal ion value), your MD system might blow up & crash (observed
problem).
Thus, if you do a "dirty & cheap" parametrization, you might even not
be able to get a MD trajectory. Consequently, I think you should pay
the price of a rigorous parametrization for your metal complex.
This is just my personal opinion based on MD simulations...
regards, Francois
> 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
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Received on Mon Jan 18 2010 - 04:00:02 PST
