[gmx-users] GROMACS nucleic acid sim. using GROMOS87

Luke Czapla czapla at rutchem.rutgers.edu
Wed Nov 27 00:00:09 CET 2002


  I'm trying to simulation a nucleic acid/protein system using the
standard GROMOS87 (default united atom) force field in GROMACS.  I want to
change the residue identifiers from DADE for adenine in DNA to just A (the
convention in PDB files for nucleic acids) in the GROMOS87 implementation,

  I tried to do this by editing ffgmx.rtp (in /usr/share/gromacs/top from
the RPM distribution package - we're in linux) and changing the [ DADE ]
to [ A ] but it still thinks DADE is the correct terminology.  I was
wondering if anyone knows what I am doing wrong and what issues are
involved in the nucleic acid simulations using GROMACS.

Luke Czapla

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