[gmx-users] DNA and GROMACS/GROMOS87

John Kerrigan kerrigje at UMDNJ.EDU
Wed Nov 27 14:58:48 CET 2002

Luke and Anton-

I've had success with DNA using the procedure that Anton described.  It's
a pain, but just go and edit your file in a text editor that has a Find/Replace
 command and make the appropriate substitutions.  Once you make the
appropriate substitutions and make sure that the residue names are aligned
in their proper columns in the PDB file (very important!), pdb2gmx will
set everything up perfectly.

RNA is a different story.  GROMACS is missing several parameters for
uracil in its parameter set.  This leads to all kinds of fun errors. I
started working on this at the end of the summer, then classes started,
etc.  I haven't had time to work on this problem. :(  



John E. Kerrigan, Ph.D.

Department of Pharmacology
University of Medicine and Dentistry of New Jersey
675 Hoes Lane
Piscataway, NJ 08854 USA

(732) 235-4473  phone
(732) 235-5252  fax

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