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Date: Wed, 29 Aug 2001 13:01:56 -0500 (CDT)
From: Vemparala Satyavani <vani # - at - # reef.phys.lsu.edu>
To: chemistry:~at~:ccl.net
Subject: initial PDB file-bond distances
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Hi,

iam writing a small code (using AMBER parameters) for a protein. My
question is the bond distances of the protein(from the PDB file) are
different from the AMBER bond distances, and hence the bond potential
energy is large(protein size: ~2500 atoms, bond energy ~ 30K kcal/mol)

is this normal?i.e., the bond distances of the PDB file being so
different from the AMBER parameter bond distances ?..is there anything i
need to do with the bond distances of the PDB file before the MD code ?

Thanks
vani