Are you working for an academic institution ?
If yes, all you need for MMPBSA is Amber Tools 16 which is free of
charge for academic use ...You just need to download it and install it
I am not familiar with the details of the tutorials ... .... I just
wanted to make you aware of an important problem that was discussed
before on this list.
Best wishes
Vlad
On 03/24/2017 10:30 AM, liulr13.mails.jlu.edu.cn wrote:
> I have no AMBER 16 ... SO the ras-raf binding free energy in A3
> tutorial is reliable?
>
>
>
> ----- 回复邮件 -----
> *发信人:*Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
> *收信人:*amber <amber.ambermd.org>
> *时 间:*2017年03月24日 16时51分58秒
> *主 题:*Re: [AMBER] 发自刘兰茹的邮件
>
>
> Please use MMPBSA from Amber 16 ... Recently, we discovered a problem
> with the calculation of the electrostatic energy in earlier
> versions of
> Amber (see the thread "MMPBSA results with Amber 12 versus Amber 16"
> from October 2016 in the mailing list archive)
>
> It may be worth considering an alert about that issue in the MMPBSA
> tutorials (as well as in the Amber Tools manuals) ...
>
> Best
> Vlad
>
> On 03/24/2017 09:42 AM, 刘兰茹 wrote:
> > Hello,
> >
> > I have a question about mmpbsa. I calculated binding free energy for
> > ras-raf complex by Amber14, and the input files were downloaded
> from A3
> > tutorial website. The results of binding free energy from PB
> calculated by
> > Amber14 is about -28, which has a large difference compared with -86
> > provided in the tutorial. But the results from GB are simliar. So my
> > question is how to modify the parameters in AMBER14 so that I
> can get -86
> > for binding free energy from PB ? I have attemped to add âuse
> _sander = 1â
> > at .general , but no work.
> >
> > Thanksâ
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Vlad Cojocaru, Ph.D., Project Group Leader
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Vlad Cojocaru, Ph.D., Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Fri Mar 24 2017 - 03:30:02 PDT
