errabah fatima ezzahra wrote:
I actually getting that error to number of coordinates in coordinate
file (waterbox_ions.gro, 3797)
does not match topology (1pef.top, 3791)
Please make sure to state up front exactly what errors you're receiving. I
suspect, then, that my statement about the "NA+6" line is correct and will solve
your problem if properly spaced.
-Justin
------------------------------------------------------------------------
*De :* Justin A. Lemkul <jalem...@vt.edu>
*À :* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Envoyé le :* Mercredi 13 Juillet 2011 13h49
*Objet :* Re: Re : [gmx-users] Adding Ions
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
-- ========================================
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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--
========================================
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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