[gmx-users] error with grompp

Mon Jul 2 10:39:24 CEST 2012

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.

I also had to #include the dum.itp since I have Dummy atoms in my pdb file
simulating the membrane around the membrane protein.
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.

> 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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