Hello gromacs users! Greetings! I was running simulation of a protein with a ligand. I have created the topology for the ligand molecule with the help of PRODRG server and ran energy minimisation step successfully. But while I am running grompp before the mdrun program it is giving following error: Making dummy/rest group for T-Coupling containing 20 elements Fatal error: Not enough ref_t and tau_t values! Can you please tell me why I am getting such an error? Also what are ref_t and tau_t values? I encountered the following error after grompp: ------------------------------------------ processing coordinates... Shuffling coordinates... Entering shuffle_xv Sorting coordinates for 1 copies of molecule Protein_A Sorting coordinates for 9896 copies of molecule SOL Sorting coordinates for 0 copies of molecule K Sorting coordinates for 0 copies of molecule Na Sorting coordinates for 0 copies of molecule Ca Sorting coordinates for 0 copies of molecule Mg Sorting coordinates for 0 copies of molecule Cl Sorting coordinates for 0 copies of molecule Zn Sorting coordinates for 1 copies of molecule FRA Warning: atom names in pla_drg.top and after_em.gro don't match (OW - HW1) Warning: atom names in pla_drg.top and after_em.gro don't match (HW1 - HW2) Warning: atom names in pla_drg.top and after_em.gro don't match (HW2 - OW) Warning: atom names in pla_drg.top and after_em.gro don't match (OW - HW1) Warning: atom names in pla_drg.top and after_em.gro don't match (HW1 - HW2) Warning: atom names in pla_drg.top and after_em.gro don't match (HW2 - OW) Warning: atom names in pla_drg.top and after_em.gro don't match (OW - HW1) Warning: atom names in pla_drg.top and after_em.gro don't match (HW1 - HW2) Warning: atom names in pla_drg.top and after_em.gro don't match (HW2 - OW) Warning: atom names in pla_drg.top and after_em.gro don't match (OW - HW1) Warning: atom names in pla_drg.top and after_em.gro don't match (HW1 - HW2) Warning: atom names in pla_drg.top and after_em.gro don't match (HW2 - OW) Warning: atom names in pla_drg.top and after_em.gro don't match (OW - HW1) Warning: atom names in pla_drg.top and after_em.gro don't match (HW1 - HW2) Warning: atom names in pla_drg.top and after_em.gro don't match (HW2 - OW) Warning: atom names in pla_drg.top and after_em.gro don't match (OW - HW1) Warning: atom names in pla_drg.top and after_em.gro don't match (HW1 - HW2) Warning: atom names in pla_drg.top and after_em.gro don't match (HW2 - OW) Warning: atom names in pla_drg.top and after_em.gro don't match (OW - HW1) Warning: atom names in pla_drg.top and after_em.gro don't match (HW1 - HW2) (more than 20 non-matching atom names) WARNING 2 [file "pla_drg.top", line 8006]: 14236 non-matching atom names atom names from pla_drg.top will be used atom names from after_em.gro will be ingnored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # ANGLES: 7484 # PDIHS: 3470 # IDIHS: 3180 # LJ14: 6948 # CONSTR: 3840 # SETTLE: 19792 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /opt/soft/gromacs/share/top/aminoacids.dat There are: 9898 OTHER residues There are: 123 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... Making dummy/rest group for T-Coupling containing 20 elements Fatal error: Not enough ref_t and tau_t values! ----------- thanking you! "praise the lord!" With prayers, prettina _____________________________________________________________ I use Krify Mail - http://mail.krify.com Get yourmail at Krify today!