AMBER Archive (2009)

Subject: Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy

From: jacky zhao (jackyzhao010_at_gmail.com)
Date: Wed Jun 03 2009 - 08:44:12 CDT


That's a good news

2009/6/3 Marc Baaden <baaden_at_smplinux.de>

>
> Dear Xueqin Pang,
>
> I have been working on some scripts (derived from the original
> Amber ones) to carry out mm-pbsa analysis with Gromacs. At the present
> stage (sort of beta-testing) these scripts are not yet publicly available.
> Anybody interested can contact me directly for more details.
>
> Sincerely,
> Marc Baaden
>
> http://www.baaden.ibpc.fr
>
> >>> xueqin pang said:
> >> Hello everyone,
> >> Since AMBER may not be suitable for molecular dynamics of protein in
> lipide
> >> membrane, I want to know if we can=C2=A0use GROMACS or NAMD for MD,
> and th
> >> en use MM-PBSA to culculate binding energy
> >> Thanks very much
>
>
> --
> Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
> mailto:baaden_at_smplinux.de - http://www.baaden.ibpc.fr
> FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
>
>
>
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>

-- 
Lei Zhao, Ph.D.
International Joint Cancer Institute of the Second Military Medical
University
National Engineering Research Center for Antibody Medicine
New Library Building 11th floor,800 Xiang Yin Road
Shanghai 200433
P.R.China
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