[gmx-users] pdb2gmx error due to terminal capping of peptide

[Neena Susan Eappen]

Hi GMX users,


  1.  I drew the structure of my target peptide on Pymol, added amide capping group (NHH) at C terminus of peptide
  2.  Typed in the command: gmx pdb2gmx –f A15K.pdb –o A15K.gro –ter –ignh
  3.  Chose AMBER99sb-ildn force field which has parameters for NH2 capping group
  4.  Fatal error
  5.  Changed naming of amide group in .rtp file of AMBER99sb-ildn from NH2 to NHH so that naming is similar to .pdb file.
  6.  Still fatal error.
The residues in the chain ALA16--NHH32 do not have a consistent type. The first residue has type 'Protein', while residue NHH32 is of type 'Other'. Either there is a mistake in your chain, or it includes nonstandard residue names that have not yet been added to the residuetypes.dat file in the GROMACS library directory.

Any insight would be appreciated,
Thank you,
Neena