Hi,
On Mon, Sep 26, 2011 at 10:08 PM, fatahiya <fatahiyamohdtap.yahoo.com> wrote:
>>average md91.pdb pdb
Since the 'average' command averages coordinates over all input
frames, it's not surprising that the resulting PDB seems distorted.
For example, if you have a methyl group that is rotating freely and
you average its coordinates over all frames, the hydrogen atoms will
appear "squished" towards the center of rotation.
2JUQ.pdb is not only missing some atoms compared to md91.pdb, but the
atom ordering within residues is different as well. You should create
a parm/restart file from 2JUQ.pdb using tleap. You could also
calculate an RMSD using cpptraj, which allows the use of multiple
topologies (you can specify a separate mask for the reference
structure as well). RMSD can be calculated as long as the target mask
and the reference mask specify the same number of atoms in the same
order. Since the residue ordering is the same in both you could for
example calculate backbone CA RMSD:
parm 2JUQ.pdb
reference 2JUQ.pdb parmindex 0
parm md91.pdb
trajin md91.pdb parmindex 1
rms CArmsd reference .CA out rmsd.dat
Hope this is helpful.
-Dan
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Received on Tue Sep 27 2011 - 06:00:03 PDT
