AMBER Archive (2009)

Subject: [AMBER] (no subject)

From: Lake, Thomas (
Date: Fri Jan 16 2009 - 11:38:09 CST


I am trying to model a cyclic peptide, so I loaded the pdb into LEAP. I
then created a bond between the two terminal residues, and then altered
the partial charges and the atom types of these residues. In LEAP this
seemed to work fine; I then created topology and coordinate files using
saveamberparm. However when I loaded these into VMD, the bonds where
the termini were linked are now massively distorted. In the LEAP editor
there doesn't seem to be this problem. Can anyone help me.


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