Ah, okey thank you. I will try to install it again. I made the changes of the files exactly as it is descriped on the site you wrote me. I send you in the last mail my changes in the files. Do you think they are okey? I was not completely sure about atomtype and residuetype and so on.
Best, Eva > On 07/02/2012 07:00 PM, [email protected] > wrote: >> 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 > > amber03.ff/tip3p.itp has never contained that - you've taken it from the > top-level $GMXLIB directory, from which it can't be moved, and can't > work with AMBER force fields. This completely explains your symptoms. > Since none of those _FF_* are defined, there's no water-related content > in your .top file. However you have constructed your amber03.ff is > wrong. I'd strongly suggest getting a new copy of amber03.ff (possibly > after upgrading to GROMACS 4.5.5) and starting again. The diff tool may > be your friend here. > >> I additionally included the dum.itp file since grompp seems not to >> "read" >> the changes I made in the several files. > > Then you've done something wrong. > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field > contains the kind of procedure you need to follow. > > Mark > >> 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, [email protected] >>> 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, [email protected] >>>>> 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, >>>>>>> [email protected] >>>>>>> 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, [email protected] >>>>>>>>> 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 [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? 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