RMSD and merging trajectories

From: Falgun Shah (fhshah_at_olemiss.edu)
Date: Sat Jan 24 2009 - 17:20:27 CST

Dear sir

I am trying to calculate per residue rmsd. The protein i am using has 3
residues with negative indexes. so when i execute "rmsd_residue_over_time
top $sel_resid" i am getting following error: atomselect: cannot parse
selection text: protein and resid -3 and noh

i have 3 segment in the pdb file. Please let me know how to deal with the
issues. Also, i wanted to know how to merge trajectories from previous run
for RMSD or energy analysis (trajectories generated during different time


Falgun H shah
PhD candidate (3rd year)
Department of Medicinal Chemistry
2028, Natural Product Center
University of Mississippi
Ph No: 6629151286(O)
          662 801 5667(M)
email: fhshah_at_olemiss.edu

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