[gmx-users] g_rms problem
chris.neale at mail.utoronto.ca
Sun Oct 28 13:19:02 CET 2012
How many atoms are in each .pdb file?
for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |head
for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |tail
-- original message --
I've 1000 separate pdb files generated by other Rosetta and I would
like to calculate the RMSD between them. I use command:
cat *.pdb > all
mv all all.pdb
to merge it.
then I use g_rms to calculate the rmsd between them:
g_rms -f all.pdb -s 0001.pdb -o rmsd.xvg
However, g_rms only give one rmsd value for it with following messages:
warnings: if there are broken molecules in the trjectory file, they can
not be made whole without a run input file
reading frame 0 time -1.0000
Warning: topology has 1840 atoms, whereas trjectory has 7360 '',. 7360 atoms
I am just wondering how can I make g_rms works fine correctly?
thank you very much
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