[gmx-users] missing atoms

ninoo mani ninoomani at yahoo.co.in
Tue Aug 1 08:21:48 CEST 2006

Dear gmx users
  I have a protein molecule with few missing residues,
  a Lys with CG, CD, CE, NZ missing atoms, and
  a Val with CG1, CG2 missing atoms.
  I noticed that pdb2gmx reads the pdb file and places the missing atoms.
  First I want to know whether gromacs places only missing atoms or it places the entire side chain? 
  Second, is gromacs' repaired molecule reliable for simulation or I should do homology modelling using other softwares to repair the molecule?

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