[gmx-users] No such moleculetype NA+

[John Wesly . J]

Have a look at the rtp file of the force field u r using for correct
representation of the ion used..

With regards,
 J. John Wesly,
 FInal Year, B.Tech., Bioinformatics,
 School of Chemical and Biotechnology,
 SASTRA University, Thanjavur,
 Tamil Nadu, India.

<~WesFaith~>
"He who desire to learn, pursues towards edification... One who has will to
do, finds a way how to do.
  Have a LEARNING SPREE.... Desire to learn... Passion to know things...
Unravel the mysteries about your abilities... "


On Sun, Dec 26, 2010 at 12:26 PM, shikha agarwal <shikhaiiitabi at gmail.com>wrote:

> hello ,
>
> this is my ions.itp file for gromos53a6 forcefield
>
> [ moleculetype ]
> ; molname    nrexcl
> CU1        1
>
> [ atoms ]
> ; id    at type    res nr     residu name    at name  cg nr    charge
> mass
> 1    CU1+    1    CU1        CU     1    1     63.54600
>
> [ moleculetype ]
> ; molname    nrexcl
> CU        1
>
> [ atoms ]
> ; id    at type    res nr     residu name    at name  cg nr    charge
> mass
> 1    CU2+    1    CU        CU     1    2     63.54600
>
> [ moleculetype ]
> ; molname    nrexcl
> ZN        1
>
> [ atoms ]
> ; id    at type    res nr     residu name    at name  cg nr    charge
> mass
> 1    ZN2+    1    ZN        ZN     1    2     65.37000
> this  is my ions.itp
>
> [ moleculetype ]
> ; molname    nrexcl
> MG        1
>
> [ atoms ]
> ; id    at type    res nr     residu name    at name  cg nr    charge
> mass
> 1    MG2+    1    MG        MG     1    2     24.30500
>
> [ moleculetype ]
> ; molname    nrexcl
> CA        1
>
> [ atoms ]
> ; id    at type    res nr     residu name    at name  cg nr    charge
> mass
> 1    CA2+    1    CA        CA     1    2     40.08000
>
> [ moleculetype ]
> ; molname    nrexcl
> NA        1
>
> [ atoms ]
> ; id    at type    res nr     residu name    at name  cg nr    charge
> mass
> 1    NA+    1    NA        NA     1    1     22.9898
>
> [ moleculetype ]
> ; molname    nrexcl
> CL        1
>
> [ atoms ]
> ; id    at type    res nr     residu name    at name  cg nr    charge
> mass
> 1    CL-    1    CL        CL     1    -1     35.45300
>
>
>
>
> for adding ions I used this command ...
>
> genion -s ions.tpr -o system_solv_ions.gro -p grompp.top -pname NA+ -np 11
> -nname CL-
>
> now when I m doing EM then getting this error
>
> grompp -f minim.mdp -c system_solv_ions.gro -p grompp.top -o em.tpr
>
> Fatal error:
> No such moleculetype NA+
>
>
> help me !
>
> regards:
> shikha
>
>
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