Dear FrancoisŁ¬
Thanks for your advice! But i still have some questions for your help. At first, i want to make the zinc atom bond to the HIS through the ZN--NB,and make the HIS a nonstandard residue,but i cannot find the point charge for the residue. I know the R.E.D. Server that you mentioned could solve the problem ,is that right ? i also tried to use the R.E.D. Server but it is very hard for me a beginner . If there are other method except this?
The second question is if i bond the zinc to the residues around it where can i find the parameters ,for example the angles and the dihedrals ?
I also want to know i deal with my system llke this is right or wrong !
Thanks for you help in advance !
Kk Zhu
At 2011-09-20 17:14:09,FyD <fyd.q4md-forcefieldtools.org> wrote:
>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 Wed Sep 21 2011 - 00:30:02 PDT
