backbone constraint

From: Urszula Uciechowska (urszula.uciechowska_at_biotech.ug.edu.pl)
Date: Wed Jul 22 2015 - 02:59:37 CDT

Dear all,

I trying to apply the harmonic constraint on my backbone atoms (CA, N, C,
O). How should I prepare the constraint file? What should be there?
I created the file with those atoms but after running namd I got an error
message:

Infiniband support is active.
Namd ibverbs will be loaded by 'apps/namd/2.9'.
 'compilers/gcc/4.8.0' load complete.
 'tools/openmpi/1.6.5-gnu-4.8.0-ib' load complete.
 'apps/namd/2.9' load complete.
 'tools/scratch/1.0' load complete.
Charmrun> started all node programs in 1.267 seconds.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Number of atoms in constraint constant PDB doesn't
match coordinate PDB

Fatal error on PE 0> FATAL ERROR: Number of atoms in constraint constant
PDB doesn't match coordinate PDB

mpiexec: killing job...

best regards
Urszula

University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk
Poland

-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/

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