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
Received on Wed May 01 2002 - 10:23:19 PDT
