[gmx-users] Adding Ions

[Justin A. Lemkul]

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 <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
>  >>
>  >> 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

========================================