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

ABEL Stephane Stephane.ABEL at cea.fr
Sun Jan 14 15:23:35 CET 2018

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

Thank for your help


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