AMBER Archive (2008)

Subject: Re: AMBER: pairwise interaction energies

From: Alessandro Nascimento (al.s.nascimento_at_gmail.com)
Date: Mon Oct 13 2008 - 05:35:39 CDT

If you're using amber9, you can try com compile and use anal :

$ cd $AMBERHOME/src/anal
$ make
$ make install

OR

you can try to compute interaction (potential) energies using VMD,
loading both your prmtop and trajectory file (vmd supports formatted
mdcrd and netcdf file formats) in the module NAMDEnergy. That works
pretty well !!!

OR

you can try to compute interaction energies using mm_pbsa.pl script
which comes with amber. See $AMBERHOME/src/mm_pbsa/Examples folder for
some examples.

PS: I've been using amber9. If you have amber10, double check if the
paths I provided are actually correct!!!

Hope this helps,

--alessandro

On Mon, Oct 13, 2008 at 4:12 AM, Thomas Leonard
<thomasj_at_bii.a-star.edu.sg> wrote:
> Hi,
> How to calculate pairwise interaction energies of the residues without GB.
>
> This can be done in amber using Anal module, but this module is no more.
>
> any suggestion/help is welcome
>
> Thomas
>
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