Hi Justin, thank you for your answer. So you mean that I should only name NA and CL like this:
genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1 -neutral -pname NA -nname CL But when I now want to run the alraedy mentioned grompp command I get the error: No such moleculetype NA Can this be because of the wrong including order? I included everything this order: ; Include forcefield parameters #include "amber03.ff/forcefield.itp" ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "amber03.ff/tip3p.itp" ; Include topology for ions #include "amber03.ff/ions.itp" #include "amber03.ff/spc.itp" #include "amber03.ff/dum.itp" Bests Eva > > > On 6/29/12 8:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> 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. >> > > Well, it is a correct outcome of genion, but it is incorrect usage. From > genion -h: > > "The ion molecule type, residue and atom names in all force fields are the > capitalized element names without sign. This molecule name should be given > with -pname or -nname, and the [molecules] section of your topology > updated > accordingly, either by hand or with -p. Do not use an atom name instead!" > > -Justin > >> 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 >> >> > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > -- > 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 > -- 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
