[AMBER] Using MM-PBSA to find binding free energy for Zif268-DNA complex

From: Roza M <m.roza88.yahoo.com>
Date: Mon, 2 Jun 2014 06:20:04 -0700 (PDT)

Dear Soumendranath Bhakat, I already have the parameters for Zn , thank you very much for telling me where to write it . It worked :) Many Thanks, Roza On Monday, June 2, 2014 3:12 PM, Soumendranath Bhakat <bhakatsoumendranath.gmail.com> wrote: I think Zn is one of the cofactor attached with your complex. Zn parameter you can get easily by googling previous Amber questions as well as any chemistry workbook. Add line here mm_pbsa_calceneent.pm hopefully it should work. On Mon, Jun 2, 2014 at 1:27 PM, Jason Swails <jason.swails@gmail.com> wrote: > On Mon, 2014-06-02 at 04:04 -0700, Roza M wrote: > > Dear amber users, > > > > > > I am trying to calculate the binding free energy for Zif 268-DNA > > complex using MM-PBSA, but I couldn't because it gives me the > > following : " no radius found for ZN " , In which file should I write > > the radius for Zn atom? > > What kind of calculation are you running?  What is your input file? > What is your exact error message? > > -- > Jason M. Swails > BioMaPS, > Rutgers University > Postdoctoral Researcher > > > _______________________________________________ > AMBER mailing list > AMBER@ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > -- Thanks & Regards; Soumendranath Bhakat _______________________________________________ AMBER mailing list AMBER@ambermd.org http://lists.ambermd.org/mailman/listinfo/amber

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Received on Mon Jun 02 2014 - 06:30:04 PDT
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