AMBER Archive (2002)

Subject: Amber7 nmode

From: Sue Heavner (sheavner_at_hsc.wvu.edu)
Date: Wed May 01 2002 - 12:23:19 CDT

Dear amber users:
I ran mm_pbsa in amber7 and with MM, GB, and NM set to 1. When the run finished I discovered that the various energy terms were calculated but the entropy terms from nmode were missing. The log file indicates that MM/GB/SAS were calculated, minimization was carried out, and the entropy calculated for each snapshot. I then went to the test directory , ran make test.nmode, and recieved the following messages:

cd nmode; ./Run.ala-dipeptide
 
NMODE: find normal modes
diffing vibs.out.save with vibs.out
PASSED
==============================================================
 
NMODE: find Langevin modes
diffing lvibs.out.save with lvibs.out
PASSED
==============================================================
diffing lmode.head.save with lmode.head
PASSED
==============================================================
 
        cd newton_raph; ./Run.newton_raph
diffing nmd_min.out.save with nmd_min.out
PASSED
==============================================================
        cd quasih; ./Run.quasih
 Title in input file: rdparm transformed trajectory
diffing quasih.out.save with quasih.out
PASSED
==============================================================
Then I went to the test/nmode directory but no files were created. When
make test.<program-name> is run for other modules of amber output is found in the corresponding directories. Thanks in advance for any help on this subject.
Sue Heavner