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

From: Holger Gohlke <gohlke_at_scripps.edu>
Date: Wed 28 Aug 2002 11:36:51 -0700

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


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
Received on Wed Aug 28 2002 - 11:36:51 PDT
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