[gmx-users] error with grompp

[Mark Abraham]

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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