[gmx-users] No such moleculetype NA+

shikha agarwal shikhaiiitabi at gmail.com
Sun Dec 26 07:56:16 CET 2010


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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