[gmx-users] Re:Moleculetype SOL contains no atoms

Tue Nov 27 03:16:08 CET 2007

The top file is 
#include "ffgmx.itp"
#include "tip5P.itp"

[ system ]
Pure water

[ molecules ]
SOL 258
-------------------------------------

The itp file is
[ moleculetype ]
; molname   nrexcl
SOL         2

[ atoms ]
; id    at type res nr  residu name   at name    cg nr   charge
#ifdef _FF_OPLS
   1     opls_118    1    SOL      OW         1       0
   2     opls_119    1    SOL      HW1        1       0.24
   3     opls_119    1    SOL      HW2        1       0.241
   4     opls_120    1    SOL      LP1        1      -0.241
   5     opls_120    1    SOL      LP2        1      -0.241

[ settles ]
; i     funct   doh     dhh
1       1       0.09572 0.15139

[ dummies3 ]
; The position of the dummy is computed as follows:
;
; The distance from OW to OL is 0.07 nm, the geometry is tetrahedral
; (109.47 deg)
; Therefore, a =3D b =3D 0.07 * cos (109.47/2) / | xOH1 + xOH2 |
;            c =3D 0.07 * sin (109.47/2) / | xOH1 X xOH2 |
;           =20
;
; Using | xOH1 X xOH2 | =3D | xOH1 | | xOH2 | sin (H1-O-H2)
;       | xOH1 + xOH2 | =3D 2 | xOH1 | cos (H1-O-H2)
; Dummy pos x4 =3D x1 + a*x21 + b*x31 + c*(x21 X x31)

; Dummy from                    funct   a       b               c
4       1       2       3       4       -0.344908  -0.344908  -6.4437903493
5       1       2       3       4       -0.344908  -0.344908   6.4437903493

[ exclusions ]
1       2       3       4       5
2       1       3       4       5
3       1       2       4       5
4       1       2       3       5
5       1       2       3       4
#endif
----------------------------------------------------------------------------

Can anyone help me in this regard?

Jestin Mandumpal
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071127/2acca475/attachment.html>