[gmx-users] error with grompp
reisingere at rostlab.informatik.tu-muenchen.de
reisingere at rostlab.informatik.tu-muenchen.de
Mon Jul 2 14:07:00 CEST 2012
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, reisingere at rostlab.informatik.tu-muenchen.de
> 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, reisingere at 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, reisingere at 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,
>>>>>>> reisingere at 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, reisingere at 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
>>>>>>>>>
>>>>>>>>> ========================================
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
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