[gmx-users] creating .tpr file

[David van der Spoel]

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 
> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/1846186_1839156/1845568/1?PARTNER=3&OAS_QUERY=null 
> target=new >
> 
> 
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> 
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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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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