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

[Justin Lemkul]

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.

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

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 
problem.

-Justin

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

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