Quoting priya priya <priyaanand_27.yahoo.co.in>:
> I am looking for some way to prepare pdb files for a molecule with
> unusual amino acid, that is not incluede in Xleap of Amber.
> Can anybody suggest me some tool that can be use to draw the molecule.
Usually when you want to develop a new FF library for a central
fragment of an unusual amino acid (AA) you start from the dipeptide
ACE-AA-NME.
You can use XLEaP to build this dipeptide:
DIPEPTIDE = sequence {ACE ALA NME}
You edit DIPEPTIDE & add graphically the missing atoms/modify the atom
names/atom types etc... You can use ALA as the 'beginning' of your new
AA if your new AA is L; otherwise you will have to fly the chirality
of ALA.
savepdb DIPEPTIDE dipeptide.pdb
regards, Francois
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Received on Fri Sep 26 2008 - 05:08:16 PDT
