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

Hi, Leave the rtp the way it was and name the residue in the pdb file so that it matches. Then you won't have to teach pdb2gmx that your newly invented residue is protein Mark On Fri., 25 Jan. 2019, 05:51 Neena Susan Eappen, < neena.susaneap...@mail.utoronto.ca> wrote: > Hi GMX users, > > >

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

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.