Dear Souvik Sur,
> I want to make a library of long chain PNA-DNA duplex which contains
> modified bases in PNA-strand,
In general, one does not build a library for a polymer/oligomer but
for each repetitive unit belonging to this polymer/oligomer.
> I have made the library of my modified base in xleap using Amber9
> and ff99bsc0 forcefield,now how can I make the long chain sequence
> of that(PNA-strand) so that I can proceed further to make the
> duplex library. Please suggest me the right path.
The FF libraries (representing the different units of your polymer)
loaded in LEaP have to match the residue and atom names found in the
PDB file (containing your polymer/oligomer).
R.E.D. and R.E.D. Server available .
http://q4md-forcefieldtools.org/
have been designed to create a set of force field libraries for any
type of natural/modified polymer.
regards, Francois
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Received on Sun Oct 16 2011 - 07:00:06 PDT
