[gmx-users] pdb2gmx does create bonds b/w DNA bases!

Azazel S'irim azizelo at yahoo.com
Wed Nov 19 20:37:01 CET 2003

For some reason, the files I downloaded are missing
enteries for bonds and angles, but do have it for
I had another dillema.  Is GROMOS96 the best force
field for DNA/RNA?  And if there is a better one, is
it easy to make it understandable to GROMACS?
I made specific 5' terminus residue types to deal with
the 5' OH that I have.  Is there a more sane way of
doing this, something like CNS's method of 'linking'? 
Thanks for all the help.

Tinoush Moulaei
School of Chemistry and Biochemistry
Georgia Institute of Technology

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