Thank you for your answer. I tried it only with NA and CL and it also didn't work. Now I have the same error with NA
Bests Eva > > > Hi, > > Check out the order of sections which you have included in your .top file. > I always got this error because of the wrong orders of sections. > > > > > Cheers, > Shima > > > ________________________________ > From: "[email protected]" > <[email protected]> > To: [email protected] > Sent: Friday, June 29, 2012 5:24 PM > Subject: [gmx-users] error with grompp > > 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 [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
