On Tue, Aug 21, 2007, Lili Peng wrote:
>
> Thanks for your help. I did convert the MOL2 file into PDB format, however,
> the bonds I manually added between the C and N atoms in glutamic acid side
> chain residues were missing in the PDB file.
OK...I didn't notice that you have N atoms on the side chains (if I read your
mail correctly). You can of course add bonds manually in tleap, but if this
is *not* a standard GLU residue, you will need to use antechamber (or
something) to get the charges and force field parameters you will need. You
should still probably break the molecule into residues, but this now sounds
like a fairly complex problem. There are some instructions for creating
non-standard residues at
http://amber.scripps.edu/antechamber.
Remember that all atoms in a given residue must have unique atom names. This
is one reason for trying to keep residues fairly small.
...dac
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Received on Sun Aug 26 2007 - 06:07:11 PDT
