Content of the ipt3p.itp file: ; This file is for backward compatibility only. ; Please directly include the tip3p.itp file from your force field directory. #ifdef _FF_GROMACS #include "gmx.ff/tip3p.itp" #endif #ifdef _FF_GROMOS96 #include "gromos43a1.ff/tip3p.itp" #endif #ifdef _FF_OPLS #include "oplsaa.ff/tip3p.itp" #endif
I additionally included the dum.itp file since grompp seems not to "read" the changes I made in the several files. I still get the error that the atomtype "DUM" is not known. The dummy atoms in the .gro file look like this: 314DUM DUM 4942 4.007 4.409 4.090 my changes are: atomtypes.atp: DU 1.00000 ; Dummy atom for the membrane DUM 1.00000 ffnonbonded.itp: DU 0 1.0000 0.0000 A 0.00000e+00 0.00000e+00 DUM 0 1.0000 0.0000 A 0.00000e+00 0.00000e+00 aminoacids.rtp: [ DUM ] [ atoms ] DUM DU 0.00 1 residuetypes.dat: DUM Protein vdwradii.dat: ??? D 0.15 Is there any problem why it should not "read" my changes? > On 07/02/2012 06:39 PM, reising...@rostlab.informatik.tu-muenchen.de > wrote: >> My topology file looks like this: >> >> 4924 4940 4939 4941 4 >> >> ; Include Position restraint file >> #ifdef POSRES >> #include "posre.itp" >> #endif >> >> ; Include water topology >> #include "amber03.ff/tip3p.itp" >> >> #ifdef POSRES_WATER >> ; Position restraint for each water oxygen >> [ position_restraints ] >> ; i funct fcx fcy fcz >> 1 1 1000 1000 1000 >> #endif >> >> ; Include topology for ions >> #include "amber03.ff/ions.itp" >> >> #include "amber03.ff/dum.itp" >> >> [ system ] >> ; Name >> Protein in water >> >> [ molecules ] >> ; Compound #mols >> Protein_chain_A 1 >> DUM 20088 >> SOL 13486 >> >> >> So I don't think that the #include of the itp3p is wrong. > > OK, and what's inside it? > >> I also had to #include the dum.itp since I have Dummy atoms in my pdb >> file >> simulating the membrane around the membrane protein. > > Well, this is non-standard, but I can't see how it would matter. > >> I already included the dummy atoms in the files atomtypes.atp, >> ffnonbonded.itp, aminoacids.rtp, residuetypes.dat and vdwradii.dat. >> So I was puzzled that it didn't know the atomtype "dum" during the >> grompp >> run. > > So what purpose is being served by that dum.itp? > > Mark > >> >> >> >>> On 07/02/2012 06:12 PM, reising...@rostlab.informatik.tu-muenchen.de >>> wrote: >>>> 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. >>> The only thing that makes sense is to use only amber03/tip3p.itp, like >>> Justin said. It defines the SOL [moleculetype], so your observations do >>> not seem consistent with #including such a file. Your .top fragment >>> suggests you're #including them at quite different points, and maybe >>> the >>> point at with you #include tip3p is inappropriate (e.g. inside an >>> #ifdef). >>> >>> Mark >>> >>>> 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? 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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