[gmx-users] Problem fpr building a peptide with two modified residues with amber ff

Justin Lemkul jalemkul at vt.edu
Sun Jan 14 15:46:15 CET 2018

On 1/14/18 9:23 AM, ABEL Stephane wrote:
> Dear all,
> I have a peptide with two modified residues at the Nter with the following sequence Mer-TYO-ILE-PHE.....GLYNH2. Mer and TYO are a cap and a modified tyrosine  residue (side chain), respectively. the Mer, TYR and ILE are bonded together with a peptide bond. To build the corresponding force field compatible with Amber. I am using pdb2gmx  with the following command (gmx5.1.2):
> pdb2gmx -f mypeptide.pdb  -p topol.top -o  mypeptide.gro
> the ILE residue are always recognized as the Nter residue of the peptide with NH3+ with the name NILE and thus I obtain the "dangling bond" error  Is it possible "to force" pdb2gmx to use a particular rtp entry (here the central ILE residue) and consequently build the correct peptide bond between the TYO and ILE residues?  Note that the name of the isoleucine residue in " mypeptide.pdb" is "ILE" and not NILE.
> I have also use pdb2gmx -f mypeptide.pdb  -p  topol.top  -rtpres yes
> but it does not work either

If Ile is being identified as the first residue, then you haven't added 
your custom residues to residuetypes.dat as Protein.


Step 5 is what people always forget (and we've made a very prominent 
warning message for the next release).

If that still doesn't work, please post the full screen output from 
pdb2gmx; it is very verbose and makes it easy to spot the origin of the 



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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