[AMBER] heavy atom rms

From: Beale, John <John.Beale.stlcop.edu>
Date: Wed, 5 Jan 2011 07:06:26 -0600

I am trying to compute and plot the heavy atom rmsd for an 81-residue protein in an MD simulation. My ptraj input file is given below:

#!/bin/csh
ptraj file.prmtop <<EOF
trajin file2.nc
rms first mass out spc_file.rms !.H= time 1.0
EOF

When I run this file the plotted output (of spc_file.rms) is a smooth curve (it looks exponential) going from an rms of 0 at t=0 and approaching y = 40. There is no structure at all in the curve. I am enclosing the plot file (spc_file.rms).

The rmsd curve for the alpha carbon atoms using a different ptraj script looks fine, giving me a plot that maximizes at about 1.5.

Would someone please look at my input file and tell me what might be wrong with it?

Thanks!

John


John M. Beale, Jr., Ph.D.
Professor of Medicinal Chemistry and Pharmacognosy
Saint Louis College of Pharmacy
4588 Parkview Place
Saint Louis, Missouri 63110
314-446-8461
Cell: 314-315-0409
FAX: 314-446-8460
jbeale.stlcop.edu<mailto:jbeale.stlcop.edu>









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Received on Wed Jan 05 2011 - 05:30:05 PST
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