AMBER Archive (2008)

Subject: AMBER: nmode/nab entropy calculations memory issues

From: chaitanya koppisetty (
Date: Tue Sep 16 2008 - 09:58:01 CDT

Dear List,

I have a question relating to entropy calculations using nmode/nab. I am
trying to calculate entropy of a protein which has around 9000 atoms. I
encountered memory problems both with nmode and nab.

I saw in "R.A. Brown and D.A. Case. Second derivatives in generalized Born
theory. J. Comput. Chem. 27, 1662-1675 (2006)." that normal mode analysis
was performed for pdb structure of 1AKD of 6370 atoms. I used nab for this
purpose and as I mentioned my system has around 9000 atoms and its
crashing with an error
>allocation failure in vector: nh = 623750625
>FATAL: allocation failure in vector()
Any estimate of how much memory I might need to run this kind of system ?

Also, I am thinking if it would be reasonable to do the calculations by
stripping of the hydrogens.(This would reduce the atom count so that there
would be no memory issues)I am not sure if the results would be
meaningful. The aim of the entropy calculations is to use it for binding
energy calculations for a protein-protein and for a protein-ligand system

I would be very glad to have any suggestions / comments.

Chaitanya, Doctoral Student,
Dept of computing science,/Inst of Biomedicine
Chalmers Univ of Tech./Gothenburg University
Gothenburg, Sweden.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)