Dear all,
I need to create topology and structure of some polypeptides with modified
amino acids (mostly attached with sugar groups). I could successfully
generate the GAFF parameters for the fragments, but I need your suggestions
about tools that can create the 3D structures of polypeptides of such
modified amino acids, preferably with controllable stereochemistry. I have
been using GUI tools like Avogadro, but it becomes cumbersome to draw the
whole chain and/or to be consistent in atom names and numbering while using
them as fragments etc.
Please advise me about the available tools (more convenient the better) to
achieve this goal. Basically I need a general purpose tool to generate an
arbitrary polymer structure given the monomer coordinates. It would be nice
if the stereochemistry (D/L) of certain atoms could be controlled as well.
Any guidance will be much appreciated. Thanks.
Best regards,
Suman Chakrabarty.
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Received on Sat Dec 13 2014 - 02:30:02 PST
