Hello I want to equilibrate water around the amino acid alanin. I guess I have no further errors up to here.
In my pdb file of alanin stands in the first line COMPND Alanin In my topology in the [ moleculetype ] block stands at name: Protein_chain_A. At the end of the topology file stands in the [ system ] block the Name: Alanin in water and in the [ molecules ] block at compund: Protein_chain_A and SOL. In my pr.mdp file for this equilibration I wrote in the output control part energygrps = Protein_chain_A and in the temperature couplin part tc-grps Protein_chain_A SOL The problem is that grompp gives me this error: Fatal error: Group Protein_chain_A not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. Does this mean that I have to make an index file first that I should gave to grompp? I don't understand why this error occurs. GROMACS should know Alanin and should know SOL? Thanks for helping me. Lovely Greetings Lara -- gmx-users mailing list gmx-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 don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
