[gmx-users] QM/MM energies

Dear gmx users, I am performing some QM/MM optimizations using the ORCA interface in order to compare the energies of different structures of the same system. However, I have some questions related with the energy terms. In the output file the "potential" and "Quantum Ener." terms are printed out

[gmx-users] pulling of a metal

= 3000 ; kJ mol^-1 nm^-2 Thanks in advance for your help Jon Mujika -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please d

[gmx-users] CMAP error

Dear Justin, Thanks for your advice. You were wright. The problem was solved adding the new residue name to residuetypes.dat The issue was that when pdb2gmx found an unknown residue name, it defined as "Others" system instead of "Protein". As a consequence, the chain was capped there, adding a CO

[gmx-users] CMAP error

Dear all, I am setting up a system with GROMACS 4.5.3 and the CHARMM force field. In the protein, I have a neutral lysine, for which CHARMM force filed has a specific residue type (LSN). When I wrote LSN as residue name in the initial pdb file, the topology file was perfectly created by pdb2gmx. H