GROMACS modification: No
Dear Gromacs Users/Developers,
I am trying to include Fluoroproline (PRF) in my peptide. I got the parameters in amber FRCMOD format and have used them to modify aminoacids.rtp file. The relevant section looks like this.
[ PRF ] [ atoms ] N N -0.146327 1 CD CT -0.189338 2 HD1 H1 0.094775 3 HD2 H1 0.094775 4 CG CT 0.420275 5 HF Hf 0.017040 6 F1 f -0.297174 7 CB CT -0.226092 8 HB1 HC 0.091203 9 HB2 HC 0.091203 10 CA CT -0.087012 11 HA H1 0.102478 12 C C 0.540229 13 O O -0.506134 14 [ bonds ] N CD N CA CD HD1 CD HD2 CD CG CG HF CG F1 CG CB CB HB1 CB HB2 CB CA CA HA CA C C O [ impropers ] CA +N C O -C CD N CA
I modified the ffbonded.itp, ffnonbonded.itp and atomtypes.atp as well. I also added the new residue to residuetypes.dat as Protein as well.
I am able to generate the system including solvation and ionization. I can also run simulations. The problem is that the backbone peptide bond between PRF and the preceding residue is not generated by pdb2gmx in the topol.top file. The peptide bond between PRF and the next residue is formed.
What could be the problem? Which files should I change so that pdb2gmx makes a bond between the modified proline and the preceding residue.
Thanks in advance.