Good Afternoon,
I'm trying to stitch together a long moiety on a serine. Due to the length
and flexiblity, I've broken up the non-standard residue into six fragments.
I would use the RED server but as of June 13 it was taken offline.
I've capped the serine, and done the geometry optimization in Gaussian, and
I attempted to use the RED-vIII.5.2 program to stitch the large thing
together. The problem is, RED-vIII only allows me to stitch two pieces
together, though I'm trying to stitch six pieces together.
Would a suitable approach be to just stitch together 6 of the pieces and
make 5 molecules as follows:
fragment 1 (serine) - fragment 2 = fragment1-2
fragment 2 - fragment 3 = fragment2-3
fragment 3 - fragment 4 = fragment3-4
fragment 4 - fragment 5 = fragment4-5
fragment 5 - fragment 6 = fragment5-6
I could then compare partial charges where they overlap of fragment12 with
fragment23, and if the difference is below a suitable threshold just stitch
the hole thing together that way? so I would get fragment1-2-3-4-5-6.
Or is there a way to do intermolecular charge fitting between more than 2
fragments with antechamber, respgen, espgen? I'm looking to avoid the above
approach if something else is more feasible.
Best Regards,
Andrew
Graduate Program in Chemical & Structural Biology
Luo Lab
University of California, Irvine
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Received on Sat Jul 01 2017 - 18:00:04 PDT
