So just entering the -pname NA and -nname CL ! Sincerely, Shima
----- Original Message ----- From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Friday, June 29, 2012 5:36 PM Subject: Re: [gmx-users] error with grompp 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
