[gmx-users] Adding Ions

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> errabah fatima ezzahra wrote:
>> i added the NA using the genion
>>     *
>>
>>       genion -s em.tpr -o waterbox_ions.gro -np 6 , and i added the NA 
>> to the topology file , subtracted the water number by 6.  tail 
>> waterbox_ions.gro file have  this
>>  3567W        W 3789   1.256   3.600   3.784
>>  3568W        W 3790   2.491   6.539   2.341
>>  3569W        W 3791   2.432   6.349   3.116
>>  3570NA      NA 3792   2.677   4.903   3.617
>>  3571NA      NA 3793   0.466   3.245   4.787
>>  3572NA      NA 3794   6.028   4.147   2.550
>>  3573NA      NA 3795   3.201   1.027   5.879
>>  3574NA      NA 3796   1.677   1.849   6.641
>>  3575NA      NA 3797   5.729   5.645   7.089
>> and the topology file
>> #include "martini_v2.1.itp"
>> #include "1pef.itp"
>> #include "martini_v2.0_ions.itp"
>> [ system ]
>>
>> ; Name
>>
>> PEPTIDE F
>>
>> [ molecules ]
>>
>> ; Compound        #mols
>>
>> Protein             6
>>
>> W                   3551
>>
>> NA+6
>>
> 
> This looks fine.  There are other things I suggested you look at; you 
> haven't ruled out that something else went wrong along the way or that 
> your peptide doesn't have the net charge you think it does.
> 

Actually, no it doesn't.  You don't have any space between the moleculetype name 
("NA+") and the number of molecules.  This line isn't being read correctly, 
which might be your problem, though I'm shocked that you're not getting some 
other error about a missing number of molecules or number of coordinates not 
matching the topology.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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