AMBER Archive (2004)

Subject: Re: AMBER: extracting energy from trajector?

From: David Smith (David.Smith_at_irb.hr)
Date: Wed Nov 24 2004 - 13:29:34 CST

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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