AMBER Archive (2004)

Subject: Re: AMBER: extracting energy from trajector?

From: MURAT CETINKAYA (cetinkayam_at_psu.edu)
Date: Sun Nov 28 2004 - 18:59:27 CST

First of all, thanks for the tips from everybody. I tried David Smith's method
but I got stuck in step 3 (described below).

In order to run the perl files i must use "./perl_name". However, in step3 i
must use two files at the same command line and i get the following message :
sh: ./enerAmber.pl: No such file or directory

I also could not set the home directory for MMTSB(probably i do not have the
permission). Is there any other way to use ensrun and enerAmber separately.

Hope my question is clear...

Thanks in advance.

On Wed, 24 Nov 2004 20:29:34 +0100, David Smith wrote:

> Hi Murat,
>
>
> > I need to extract the energy values of my system from my trajectory file
created
> > by sander. I have lost my mdout file so, I will either re-run the simulation
> > (but i do not have time for it) or find a way to get these energy data from
my
> > crd file.
>
> Another possibility is with the MMTSB toolkit
> (http://mmtsb.scripps.edu/)
>
> It is quite easy to install and quite nice to use. Apart from possibly
> solving your current problem, you may find it quite useful for lots of
> things. Depending on how sophisticated your md run was you may get away
> with something like the following:
>
> 1) convert your trajectory to pdbs with ptraj
> 2) make an ensemble directory from them:
>
> checkin.pl -dir DIR NAME NAME.pdb.*
>
> (where DIR and NAME are chosen by you)
>
> 3) recursively calculate the energy over the set e.g.:
>
> cd DIR
> ensrun.pl -set etot NAME enerAmber.pl -par
> param=ff99,gb=tc,gbsa=1,cut=0,gbeps=78.5
>
> (the last command should be all on one line and should be adjusted [if
> possible] to suit your run, the web documentation is pretty good)
>
> and then you can get the energies by:
>
> getprop.pl -prop etot NAME
>
>
> Anyway, it may seem a bit complicated but I have found it a very helpful
> toolset for lots of things.
>
> Good luck.
>
>
> --
> Dr. David Smith
> Division of Organic Chemistry and Biochemistry
> Rudjer Boskovic Institute
> Bijenicka 54
> 10002 Zagreb, Croatia
> tel: +385-1-4561252
> fax: +385-1-4561118
>
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>

Murat CETINKAYA
Biomolecular Materials Lab,
Dept. of Engr. Science and Mechanics,
The Pennsylvania State University,
University Park, PA 16802
office: (814) 863 9967
web: www.personal.psu.edu/muc176
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