AMBER Archive (2008)

Subject: AMBER: MM-PBSA/NMODE in Amber 10

From: Peterson, Matthew W. (MPETERSON) (
Date: Mon Sep 15 2008 - 15:37:41 CDT

Iım having some trouble getting normal mode calculations to work using the script in AMBER 10.

I tried running the example, and I got this:

=>> Calculating energy / entropy contributions
    Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_lig.crd.1
        Minimize structure
        /projects/BIO/sw/amber10/exe/sander -O -i -o
sanmin_lig.1.out -c ../01_GenerateSnapshots/ras_raf_II_wt_lig.crd.1 -p
../raf_wt.prmtop -r sanmin_lig.1.restrt not running properly

If I look at sanmin_lig.1.out, I find the following error:

NTXO ( 0) must be 1.

    (ntx0=0 is no longer supported)

I also was having some trouble with the binding scripts, until I followed
the solution posted here

Has anyone had any luck running these scripts "out of the box?" I'm trying
to figure out if this is a configuration error on my part, or issues with
the scripts and modules.



Matthew Peterson
The MITRE Corporation

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