[gmx-users] error with grompp
Mark Abraham
Mark.Abraham at anu.edu.au
Mon Jul 2 14:16:20 CEST 2012
On 07/02/2012 10:07 PM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> 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.
They look plausible, but the proof is in whether it works.
Mark
> 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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