[gmx-users] question about DNA simulation 5'&3' ends

Luke Czapla czapla at rutchem.rutgers.edu
Sat Nov 30 00:32:08 CET 2002

Hi all,

  I want to remove the 5' Phosphate from the 5' end and add a hydrogen to
the O3* of the 3' end of a 10bp oligonucleotide double stranded helix.  I
was wondering if I had to add this explicitly in the rtp (by making new
residues) or if there was something similar to the N and C terminii
database for this type of thing.  The only other resort I have is to
modify the pdb2gmx source code some more.

thanks again,
Luke Czapla

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