Hello,
I am trying to simulate a cyclic peptide. I have the pdb and I have built the topology using xleap:
$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
clearpdbresmap
mol=loadpdb pdb_original.pdb
saveamberparm mol mol.top mol.crd
I solvated it, but in the minimization I see that the first and last residue are separating each other.
Could anyone help me to build the topology for a cyclic peptide?
Thank you very much in advance,
Rebeca García Fandiño
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Received on Tue Jul 20 2010 - 09:00:04 PDT
