AMBER Archive (2002)

Subject: [Re: can carnal do the job as anal to break down the energy?]

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Wed Aug 28 2002 - 13:36:51 CDT

Dear Haizhen,

> This is Haizhen. I have one question to bother you. In the AMBER manual,
> it is said that CARNAL is designed to replace ANAL eventually.
Indeed, I found a related sentence, although I would say that carnal is
more a complement to anal than a substitute, since carnal does mostly
structural analyses while anal does energetic analyses.

> Now I am
> wondering how to get the energy components from mdcrd, using CARNAL, but
> not ANAL.
I'm not aware of any possibilty to do this with carnal, but somebody
else might know better?

> In Anal, you can get E-ele, E-vdw, E-bond, E-angle, E-torsions,
> and etc. from calculating the mdcrd files. Can it be done in Carnal? If
> possible, would you please tell me how? What kind of in file should be
> used? Do you have any sample in file for this type of job?
I'm not quite sure what you want to do - if you want to break down
energies for single snapshots of your trajectory into E-ele, E-vdw,
E-internal, ..., mm_pbsa should be appropriate.
If you want to post-process a whole trajectory, you might want to have a
look at the IMIN=5 option for sander. I have never used this, so others
might know more.
If you are interested in more detailled analyses of internal energies,
anal seems to be the right program.

Best regards

Holger 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
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