[gmx-users] LINCS WARNING after good minimization and equilibration (NPT and NVT)

Dear GROMACS users, I only begin to work with gromacs and now have some problems with tetra protein. I used AMBER force field and made several changes (in ffamber.rtp, specbond.dat, ffamber99bon.itp) to create an isopeptide bonds between monomers. Minimization and equilibration (NPT and NVT) were O

[gmx-users] isopeptide bond

Dear GROMACS users, I started to work with gromacs (version 4.0.5) only several weeks ago and I need your help. Now I am trying to add a new *isopeptide bone* to connect Lys and Gly (to make a dimer of *ubiquitin*). I use AMBER force field. What I did: 1. Added new type of residues to ffamber.rt