Hi everybody, I added ions to the solvent around my structure with the command:
genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA+ -nname CL- and then I select the 13 (SOL) Now I have in my topology file [ molecules ] ; Compound #mols Protein_chain_A 1 DUM 30066 SOL 14305 NA+ 32 CL- 32 which is correct in my opinion. But now when I want to run grompp: grompp -v -f minim_solv.mdp -c 3m71_minim_ion.gro -p 3m71.top -o 3m71_minim_ion.tpr 2>>logErr 1>>logOut I always get the error: No such moleculetype NA+ although I already included the ion topology file: ; Include topology for ions #include "amber03.ff/ions.itp" What is wrong here? Best Eva -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
