[gmx-users] g_rms problem

Christopher Neale 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

More information about the gromacs.org_gmx-users mailing list