[gmx-users] Adding Ions

[errabah fatima ezzahra]

Hi Justin 


when i seperated the NA+ and 6 i got this error

NOTE 1 [file em.mdp]:
  For energy conservation with switch/shift potentials, rlist should be 0.1
  to 0.3 nm larger than rcoulomb.


NOTE 2 [file em.mdp]:
  For energy conservation with switch/shift potentials, rlist should be 0.1
  to 0.3 nm larger than rvdw.

Generated 0 of the 465 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein'
Excluding 1 bonded neighbours molecule type 'W'
Excluding 1 bonded neighbours molecule type 'NA+'
Warning: atom name 3792 in 1pef.top and waterbox_ions.gro does not match (NA+ - NA)
Warning: atom name 3793 in 1pef.top and waterbox_ions.gro does not match (NA+ - NA)
Warning: atom name 3794 in 1pef.top and waterbox_ions.gro does not match (NA+ - NA)
Warning: atom name 3795 in 1pef.top and waterbox_ions.gro does not match (NA+ - NA)
Warning: atom name 3796 in 1pef.top and waterbox_ions.gro does not match (NA+ - NA)
Warning: atom name 3797 in 1pef.top and waterbox_ions.gro does not match (NA+ - NA)

WARNING 1 [file 1pef.top, line 19]:
  6 non-matching atom names
  atom names from 1pef.top will be used
  atom names from waterbox_ions.gro will be ignored

what s th difference between NA+6 And NA+        6 .



________________________________
De : Justin A. Lemkul <jalemkul at vt.edu>
À : Discussion list for GROMACS users <gmx-users at gromacs.org>
Envoyé le : Mercredi 13 Juillet 2011 13h49
Objet : Re: Re : [gmx-users] Adding Ions



Justin A. Lemkul 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

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

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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