> trajin nptm501.dcd 1 1000 20
...
> trajout 10ns.dcd
> reference m_in.pdb
> rms reference out rms.dat ":1-104.C,CA,N" time 40
Is there a 1-1 mapping in the names between m_in.pdb and your prmtop/
generated PDB's, or in other words does atom 100 in m_in.pdb correspond to
atom 100 in the prmtop? Often the atom ordering in the input PDB
(presumably from experiment or another program) is not preserved when you
build the topology/coordinates. Try using your topology/coordinates to
build a corresponding PDB with the expected atom ordering.
Alternatively, try:
rms first out rms.dat ":1-104.C,CA,N" time 40
--tec3
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 14 2009 - 08:30:04 PST
