Rebeca,
You need to bond the residues together which are at the end i.e.
bond mol.29.C mol.1.N
bond mol.1.SG mol.22.SG
This is what I did for pdb 1NB1 which is a typical cyclotide.
Cheers,
~Levi
2010/7/20 Rebeca García Fandiño <regafan.hotmail.com>
>
> 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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--
--
==
Levi C.T. Pierce, UCSD Graduate Student
McCammon Laboratory
mccammon.ucsd.edu <http://mccammon.ucsd.edu/%7Esnichols>
w: 858-534-2916
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Received on Tue Jul 20 2010 - 10:00:03 PDT
