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. I also had to #include the dum.itp since I have Dummy atoms in my pdb file simulating the membrane around the membrane protein. 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. > 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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