[gmx-users] AMBER FF naming and caps

Ebert Maximilian m.ebert at umontreal.ca
Mon Sep 29 11:59:03 CEST 2014

Dear list,

I am a little bit confused regarding the preparation needed to use the AMBER FF in GROMACS 5.0.1. I have a simple PDB file of a protein and I  use this as input to pdb2gmx. I selected the AMBER FF during the creation process:

gmx_mpi pdb2gmx -f protein.pdb -o protein_processed.gro -water spce

This generates the gro, top and itp file. Now when I open the gro file in VMD I get an unusual bond between the last two residues of the protein chain. I already figured out why this is. The last amino acid has a charged carboxylate with the atom type OC1 and OC2 which are not identified as amino acids by VMD. After further reading of the manual I found this paragraph:

The AMBER force fields have unique forms for the terminal residues, and these are incompatible with the -ter mechanism. You need to prefix your N- or C-terminal residue names with "N" or "C" respectively to use these forms, making sure you preserve the format of the coordinate file. Alternatively, use named terminating residues (e.g. ACE, NME).

Now I was thinking that I have to change the name of the N and C terminal residue. However, looking into my top file GROMACS already knows about AMBER's naming convention:

; residue 290 TRP rtp CTRP q -1.0
  4049          N    290    TRP      N   4049    -0.3821      14.01   ; qtot -6.382
  4050          H    290    TRP      H   4050     0.2681      1.008   ; qtot -6.114
  4051         CT    290    TRP     CA   4051    -0.2084      12.01   ; qtot -6.322

Now my question do I have to do anything or is GROMACS 5 taking care of the correct termini in the AMBERE FF?

Thank you very much,


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