Okey thank you. But shell I also #include "amber03.ff/spc.itp"
Because when I don't include it I get the error: Fatal error: No such moleculetype SOL An when I include it there is no error. But in one of the last mails Justin wrote that: "You're using two different water models, so things are getting overridden there. With AMBER03, you should be using TIP3P, not SPC. The conflicting water models suggest you've made manual modifications to the topology. Perhaps there is some error as a result." > On 07/02/2012 05:49 PM, reising...@rostlab.informatik.tu-muenchen.de > wrote: >> Hi Justin, >> I wanted to use the only tip3p but I do not have the tip3p.gro file but >> only the tip3p.tip file. > > http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file > >> I also have the tip4p.gro and tip5p.gro file. Can >> I also use them? > > No. > > Mark > >>> On 6/29/12 5:38 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: >>>> 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 >>>> >>> I see no reason this would not work. However, I just noticed from your >>> previous >>> message: >>> >>>>>> ; 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" >>>>>> >>> You're using two different water models, so things are getting >>> overridden >>> there. >>> With AMBER03, you should be using TIP3P, not SPC. The conflicting >>> water >>> models suggest you've made manual modifications to the topology. >>> Perhaps >>> there >>> is some error as a result. >>> >>> -Justin >>> >>> -- >>> ======================================== >>> >>> 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 > -- 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
