David,
Thanks. + follow up question.
One problem we have had is that our side chain atoms are the one's bonded to the
previous amino acid and/or following amino acid.
Is there a way to designate main chain N, CA, C atoms in the mol2 file? These are
designated by M in the prepi files.
Thanks again,
John Finke
attached mail follows:
On Fri, May 02, 2008, finke.oakland.edu wrote:
> However, the connectivities produced from a PDB of nitrotyrosine (created in
> SPARTAN) end up being incorrect. Our attempts to modify a normal tyrosine
> prepi file have also ended in problems. (Our tyrosine prepi file works well
> but once we change it, problems occur).
I suggest you use mol2 files, that are much simpler to work with than prepi
files. (We are trying to deprecate that file format anyway).
In mol2 files, you just have a list of bonds, making it easy to examine and
modify connectivities, etc.
...good luck...dac
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Received on Sun May 04 2008 - 06:07:47 PDT
