JMandumpal wrote:
Dear Gromacs users,
Using the command, grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr, I
wanted to build up tpr file for the simulation, but failed to do so.
I received the error message :
Moleculetype SOL contains no atoms.
I paste my top files and .itp file below
********************************************
1. TOP FILE
**************
#include "ffgmx.itp"
use ffoplsaa instead
#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
mobiles
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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