[gmx-users] error with grompp
reisingere at rostlab.informatik.tu-muenchen.de
reisingere at rostlab.informatik.tu-muenchen.de
Mon Jul 2 11:00:34 CEST 2012
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, 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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