Unfortunately my capping groups (NME and ACE) which I had to put in myself for the Amber forcefield in Gromacs have a long bond each. It is just long enough to throw a LINCS error, yet, running an energy minimisation does not seem to correct it (there is absolutely no change to the bond distance and I have managed to progressively reduce the energy minimisation tolerance/Fmax to 90).

I would like to change the distance in the bond whilst maintaining the .gro file format. It would be very undesirable to go through the pdb2gmx process all over again.

Any suggestions?

Thanks