Dear Kongkai Zhu,
You first need to derive charge values and generate a force field
library for your complex. You could use R.E.D. Server Development for
that .
http://q4md-forcefieldtools.org/REDS-Development/
R.E.D. Server Development/R.E.D. IV contains by now a first version of
a new QM algorithm that perform many checking on the optimized
geometry for metallic complexes (a limitation here is that the cpu
time is greatly increased...), a lot of QM jobs here...
Then, you will need to define van der Waals and bonding force field
parameters; Literature can help here.
regards, Francois
Quoting Kk Zhu <hkhhh.k.163.com>:
> Dear amber users,
>
> There is a troublesome problem which hinder me for a long time and
> i am eager for your kind help.
>
> 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!
>
> Best regards!
>
> Kongkai Zhu
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Received on Thu Sep 15 2011 - 00:30:03 PDT
