See section 5 of this tutorial for how to do an RMSD alignment with VMD:
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_nine/index.htm
This will let you compare the two structures. Alternatively you can do it
with ptraj to create a pdb that is rmsd aligned to the original structure.
All the best
Ross
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|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
snoze pa
Sent: Monday, April 17, 2006 11:20
To: amber.scripps.edu
Subject: AMBER: ambpdb and original PDB
Hi,
After minimization, i generate a PDB file using ambpdb, but the center of
PDB coordinate from ambpdb seems to different from the original PDB file.
Is it okie, because I want to compare the changes in my original PDB file
after minization. If yes then how can I overlap these two structures?
thanks in advance
snoze
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Received on Tue Apr 18 2006 - 03:02:43 PDT
