Dear kk zhu,
Yes, indeed 'you may have to justify your parameter choices at some
point'. This means choose a topology for your complex i.e. define the
bonds which are established between the ligands and the metal center.
A way to demonstrate that your choice is correct is to use quantum
chemistry and run a geometry optimization job. Yes, this type of job
is time consuming and can be complex.
R.E.D. Server provides the software and hardware to rigorously define
such a bioinorganic complex. So far, we can provide a machine with up
to 24 cores for big QM jobs (just write to us and request to use it).
Yes, you are right R.E.D. Server might remain complex to use for new
users (even if procedures are more and more automated). However, you
'only' need to prepare a P2N input file with a correct input geometry
and with correct total charge and spin multiplicity values; R.E.D.
Server and in particular now R.E.D. Server Development is built to
solve most of the problems encountered during the geometry
optimization step.
We can also help you to build your P2N file [but so far we cannot
generate the force field library instead of the user (lack of time);
we might provide this feature in the future]. You can send many
queries to the Amber or q4md-fft mailing list .
http://lists.q4md-forcefieldtools.org/wws/info/q4md-fft. We always try
to help.
regards, Francois
Quoting Bill Ross <ross.cgl.ucsf.EDU>:
> Do you think that there are effective bonding, angle, and dihedral
> potentials? Unless you can find a paper to base your choice on,
> I think you may have to justify your parameter choices at some point.
>
> Bill
>
>> Thanks for your instant reply. I know what you mean, but in my
>> system the distance between Zn and the residues is not beyond 2.35
>> Angstrom.And after i read some literature i think make them bond
>> may be better ,is that right ? so i want to know the angles and
>> dihedral and so on, if someone who had done the same system could
>> you give me the parameters, i found it is not a easy work to
>> develop it myself.
>> Thanks everyone in advance!
>> Best regards!
>> kk zhu
>>
>>
>>
>> > Date: Fri, 16 Sep 2011 08:39:20 -0700
>> > From: ross.cgl.ucsf.EDU
>> > To: amber.ambermd.org
>> > Subject: Re: [AMBER] help ! zinc parameters
>> >
>> > > Two Zinc ions was embedded in the protein which i want to
>> simulate with AMBER, the one Zinc ion coordinated with 3 HIS,and
>> the other one coordinated with HIS ,CYS ,ASP and a structure water
>> molecule.
>> > >
>> > > Unfortunately, i didn't find the corresponding parameters could
>> be used in AMBER for these two protein-metal coordination system
>> after i searched through our Mailing List and consulted the related
>> papers. As a beginner for AMBER, i have litter idea for how to get
>> or develop these parameters properly. So could someone be so
>> kindly to give me some helpful guide for this tough problem? Or
>> could someone have the similar experience and have developed these
>> parameters could be used in AMBER ff?
>> > >
>> > > Any suggestions will be greatly appreciated! Thanks everyone in advance!
>> >
>> >
>> > Since the Zns are coordinated and not bonded, maybe you could use
>> > standard residues, and enforce the coordination with nmr restraints.
>> > This would save effort in parameterizing angles and dihedrals with Zn.
>> >
>> > Bill
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Received on Tue Sep 20 2011 - 02:30:02 PDT
