[gmx-users] more questions

Luke Czapla czapla at rutchem.rutgers.edu
Mon Oct 8 23:21:58 CEST 2001

Greetings user list,

  I have some more questions, that are unrelated to the glucose-binding
protein.  I want to define a new type of residue that is formed by the
sequence Ser-Tyr-Gly, post-translationally modified through an
auto-cyclization reaction between Ser and Gly.  This is the chromophore
found in many green fluorescent proteins.  I understand that defining
new residues is best done by adding to the rtp (Residue topology file)
with proper charges that match similar structures found in the force
fields in gromacs.  
  I would like to ask about what important things must be modified for
simulations to work.  We are very much interested in hydrogen bonding, so
anything regarding changes to the hydrogen database is important, and I
have no idea if I need to edit the termini database or not to define this
new residue.  Any advice on this would be appreciated, and an example of
someone doing something like this (defining new residues) would be of
incredible help!  Thanks


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