[gmx-users] Re: Adding Ions

[Justin A. Lemkul]

errabah fatima ezzahra wrote:
> 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.
> 

These notes indicate that your .mdp settings are incorrect.  Follow the 
suggesting printed.

> 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
> 

This error is probably harmless, since you are actually using sodium and there 
isn't really a mismatch.  The name listed in the [molecules] section must match 
the name specified in the corresponding [moleculetype] directive in ions.itp, 
with constituent residues and atoms named accordingly.  In this case, ions.itp 
is specifying the atom name as "NA+" while your coordinate file uses "NA" instead.

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

Spacing.  All lines in the [molecules] directive are read as:

(moleculetype name) (some amount of space) (number of molecules)

Proper spacing is an absolute requirement for proper interpretation of the 
topology.  The amount of whitespace is unimportant, but it has to be there, 
otherwise grompp reads a continuous string and finds that there is a 
moleculetype named "NA+6" that has no molecules associated with it.

-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:
>  >
>  >
> 
>  >> 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
> 
> ========================================
> -- gmx-users mailing list    gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org 
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 

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

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

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