Dear Charles and xplor-nih users,
I am trying to get a RMSD matrix from about 400 structures. While
using the script eginput/gb1_rdc/pairRMSD.py, I got the following
error:
pairRMSD.py(82): for j in range(i+1,len(pdbFiles)):
pairRMSD.py(83): protocol.initCoords(pdbFiles[j])
PDBTool:read: atom not found in structure: AXIS ANI 500 X
PDBTool:read: atom not found in structure: AXIS ANI 500 Y
PDBTool:read: atom not found in structure: AXIS ANI 500 Z
PDBTool:read: atom not found in structure: AXIS ANI 500 OO
PDBTool:read: atom not found in structure: AXIS ANI 500 OO2
PDBTool:read: atom not found in structure: AXIS ANI 500 PA1
PDBTool:read: atom not found in structure: AXIS ANI 500 PA2
matchInexactAtomEntry: found no match for entry AXIS 500 X
pseudo atom
matchInexactAtomEntry: found no match for entry AXIS 500 Y
pseudo atom
matchInexactAtomEntry: found no match for entry AXIS 500 Z
pseudo atom
matchInexactAtomEntry: found no match for entry AXIS 500 OO
pseudo atom
matchInexactAtomEntry: found no match for entry AXIS 500 OO2
pseudo atom
matchInexactAtomEntry: found no match for entry AXIS 500 PA1
pseudo atom
matchInexactAtomEntry: found no match for entry AXIS 500 PA2
pseudo atom
%ALLHP-err: too much memory requested.
Subroutine DIE called . Terminating
When running the script, the memory usage of 'xplor' process (
using 'top' command) keeps growing. Since I only need the RMSD values,
is there any way to dump the calculated data from the memory?
(Besides, my computer has 2GB memory)
Thanks!
Yun Lin
