[gmx-users] error with grompp

[Justin A. Lemkul]

On 6/29/12 9:20 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi Justin,
> thank you for your answer.
>
> So you mean that I should only name NA and CL  like this:
>
> genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
>   -neutral -pname NA -nname CL
>

This is a correct command.

> But when I now want to run the alraedy mentioned grompp command I get the
> error:
>
> No such moleculetype NA
>

What does your [molecules] directive specify?  Have you cleaned up the topology 
from the prior (incorrect) invocation of genion/grompp?

> Can this be because of the wrong including order? I included everything
> this order:

The order of #include statements is irrelevant.  The only order that matters is 
in [molecules], which must match the contents of the coordinate file.

-Justin

> ; Include forcefield parameters
> #include "amber03.ff/forcefield.itp"
>
>
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; 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"
>
>
> Bests Eva
>
>
>
>>
>>
>> On 6/29/12 8:54 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>>> Hi everybody,
>>> I added ions to the solvent around my structure with the command:
>>>
>>> genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
>>> -neutral -pname NA+ -nname CL-
>>>
>>> and then I select the 13 (SOL)
>>>
>>>
>>> Now I have in my topology file
>>>
>>> [ molecules ]
>>> ; Compound        #mols
>>> Protein_chain_A     1
>>> DUM             30066
>>> SOL         14305
>>> NA+              32
>>> CL-              32
>>>
>>> which is correct in my opinion.
>>>
>>
>> Well, it is a correct outcome of genion, but it is incorrect usage.  From
>> genion -h:
>>
>> "The ion molecule type, residue and atom names in all force fields are the
>> capitalized element names without sign. This molecule name should be given
>> with -pname or -nname, and the [molecules] section of your topology
>> updated
>> accordingly, either by hand or with -p. Do not use an atom name instead!"
>>
>> -Justin
>>
>>> But now when I want to run grompp:
>>>
>>> grompp -v -f minim_solv.mdp -c 3m71_minim_ion.gro -p 3m71.top -o
>>> 3m71_minim_ion.tpr 2>>logErr 1>>logOut
>>>
>>>
>>> I always get the error:
>>>
>>> No such moleculetype NA+
>>>
>>>
>>> although I already included the ion topology file:
>>>
>>> ; Include topology for ions
>>> #include "amber03.ff/ions.itp"
>>>
>>> What is wrong here?
>>>
>>> Best Eva
>>>
>>>
>>
>> --
>> ========================================
>>
>> 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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>
>
>

-- 
========================================

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

========================================