[gmx-users] error with grompp

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jul 2 13:24:18 CEST 2012 

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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>

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