[gmx-users] Adding Ions
errabah fatima ezzahra
errabahf at yahoo.fr
Wed Jul 13 19:56:27 CEST 2011
I actually getting that error to number of coordinates in coordinate file (waterbox_ions.gro, 3797)
does not match topology (1pef.top, 3791)
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:
> 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
> 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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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