Hi Justin, yes I removed all the old resulting files and did everything again. So now there is the topology and coordinate file with only NA and CL and not NA+ or CL-. I also checked whether the molecules are listed in the same order as in the .gro file and it is the case. So that is also correct.
What do you mean with: > What does your [molecules] directive specify? My [molecules] part in the topology file looks like this: [ molecules ] ; Compound #mols Protein_chain_A 1 DUM 20088 SOL 13428 NA 29 CL 29 Bests, Eva > > > On 6/29/12 9:20 AM, [email protected] wrote: >> 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 >> > > This is a correct command. > >> But when I now want to run the alraedy mentioned grompp command I get >> the >> error: >> >> No such moleculetype NA >> > > What does your [molecules] directive specify? Have you cleaned up the > topology > from the prior (incorrect) invocation of genion/grompp? > >> Can this be because of the wrong including order? I included everything >> this order: > > The order of #include statements is irrelevant. The only order that > matters is > in [molecules], which must match the contents of the coordinate file. > > -Justin > >> ; 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, [email protected] 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 [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 >>> >> >> >> > > -- > ======================================== > > 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 [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
