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 Mon Sep 19 2011 - 14:00:02 PDT
