[gmx-users] pdb2gmx and DNA

Michael Brunsteiner mbx0009 at yahoo.com
Fri Nov 5 02:29:47 CET 2004

dear all,

I would like to simulate DNA with Gromacs and encounter
problems. I know this question has been asked before ...
When I use the GROMOS96 43a1 Forcefield in pdb2gmx (gmx-3.2.1)
after replacing all residue names accordingly (A->DADE, etc)
I still get numerous missing atoms.
when I look at the rtp file and compare it with various PDB files
I got from http://ndbserver.rutgers.edu/ I find that the order of
atoms (and atomnames) in pdb file and rtp entry generally do not
correspond. I tried to search the WWW for a gromos FF
compatible DNA structure files, but found nothing.
any ideas ?


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