[AMBER] problem about cyclic peptide

From: Rebeca García Fandiño <regafan.hotmail.com>
Date: Tue, 20 Jul 2010 15:33:15 +0000

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
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
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