[AMBER] Fwd: Prepare pbd file modified cyclodextrin

From: Игорь Злотников <izlotnikov2003.yandex.ru>
Date: Sun, 14 Feb 2021 15:16:16 +0300

   Â Â Â Good afternoon, Dear colleagues!
   Â Â Â I have some questions about preparing pdb files for Amber. I need to
   get
   Â Â Â cyclodextrin.pdb in amber format, so i named residues in ring 4GA.
   Then i
   Â Â Â modified CD with mannose --> residue became UGA, and mannose named
   0MA. But
   Â   now i want make CD-mannose using spacer à between CD and mannose
   Â Â Â (etilenglicol or acetamide). Problem: how named this atoms (spacer) or
   how i
   Â Â Â may convert pdb structure from pymol (or othet not Amber format) to
   amber
   Â Â Â format?
   Â Â Â Thank you!
   Â Â Â Best wishes,
   Â Â Â Zlotnikov Igor
   Â Â Â Ã
   Â Â Â Ã
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References

   1. mailto:AMBER.ambermd.org
   2. http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sun Feb 14 2021 - 04:30:02 PST