dear Justin, The link of (http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology) helped but still I have problem.
There are 35344SOL molecules in my _solv.gro file. the last atom is N2 72342. The last part of my topol.top file is: [molecules] ; compound #mols Protein_A 1 Protein_B 1 Protein_C 1 Protein_D 1 SOL 27363 NA+ 0 Then typing grompp commands gives: number of coordinates in coordinate file (a_solv.gro, 72342) does not match (topol.top, 72341) I guess that the topol.top is based on water not matching nitrogen that is why I can't balance the numbers. I also tried to run again from the begining on my case protein. this time I manipulated the topol file with these numbers: [molecules] ; compound #mols Protein_A 1 SOL 24044 NA+ 1 It started operating but: note: System has non-zero total charge: -1.000000e+00 (which is quite logical) warning: atom name 210 in topol.top and a_solv.gro does not match (OW- N) ...... WARNING 1 [file topol.top, line 37]: 72133 non matching atom names atom names from topol.top will be used atom names from a_solv.gro will be ignored Does it mean that it will replace the nitrogen solvent with water molecules? What should I do this time? Thanks. Best regards, Sarah -- 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
