AMBER Archive (2009)

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

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Tue Jun 02 2009 - 09:53:19 CDT

I believe MM-PBSA needs amber stype prmtop and crd files, so you will
need to generate those first. You can probably use ptraj to convert
the trajectory file, but I'm not sure how you would generate the
prmtop files. Once you have the files in the right format, then how
the files were generated should make no difference, from the MM-PBSA
program's standpoint.

But, be extra careful here, as there are *lots* of things that may go
wrong there.

Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
-------------------------------------------------------------------------------------------
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On Sun, May 31, 2009 at 8:47 AM, xueqin pang <pangxueqintea_at_yahoo.com.cn> wrote:
> Hello everyone,
>
> Since AMBER may not be suitable for molecular dynamics of protein in lipide membrane, I want to know if we can use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy
>
>
> Thanks very much
>
>
> ===================================================================================================
> Pang Xueqin
> State Key Laboratory of Molecular Reaction Dynamics
> Dalian Institute of Chemical Physics
> Chinese Academy of Sciences.
> Tel: +86-411-84379352 Fax: +86-411-84675584
> http://www.english.dicp.ac.cn/
> ===================================================================================================
>
>
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