[gmx-users] error with grompp

[reisingere at rostlab.informatik.tu-muenchen.de]

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

But when I now want to run the alraedy mentioned grompp command I get the
error:

No such moleculetype NA

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