[gmx-users] running unrestrained MD for tutorial

Dear Users, Re tutorial http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ After running comand: grompp -v -f pr.mdp -c 1LW9-EM-solvated.gro -p 1LW9.top -o 1LW9-PR.tpr and mdrun -v -deffnm 1LW9-PR (gave message Routine should not have been called:

[gmx-users] editconf.

Dear Users, Re Introductory tutorial; Trying to run the following: editconf -f out.gro -o fws_ctr.gro -center x/2 y/2 z/2 I get the error message, Fatal error: Expected a real argument for option -center Can anyone help, Many Thanks, David. -- gmx-users mailing listgmx-user

[gmx-users] Non standard amino acids.

Dear Users, We want to run gromacs molecular dynamics for a molecule which contains the following non standard amino acids: D-MeVal and L-Nva (norvaline) How may we proceed to parameterise these residues to include in the appropriate force field. (ffG43a2.rtp). We would be grateful for any informa