[gmx-users] problems in grompp

[David]

On Sat, 2004-09-11 at 03:02, Alok Jain wrote:
> Thanks for ur suggestion :-)
> 
> but now i am facing new problem :-(
> when i try to run grompp program i am getting following error.
> Fatal error: number of coordinates in coordinate file (dppc128.gro, 11296)
>              does not match topology (dppc128.top, 17365)
> 
You don't have all atoms in your gro file and/or you have the atoms but
have not updated the number of atoms on the second line in the gro file.




> before  this  i made the dppc128.top file, by using bffgmx_lipids.tar.gzy 
> force field  which is as  follows:-
> 
> ; topology for a pure DPPC bilayer with 128 lipids and 3655 SPC water ;
> molecules
> #include "/root/dppc/ffgmx.itp"
> ;#include "lipid.itp"
> #include "/root/dppc/dppc.itp"
> 
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
> 
> [ system ]
> ; name
> Pure DPPC bilayer with 128 lipids and 3655 water molecules
> 
> [ molecules ]
> ; name	number
> DPPC    128
> SOL     3655
> 
> 
> After that i generate the .gro file by using editconfo program :-
> editconf -f dppc128.pdb -o dppc128.gro
> which contain
> 11296 atoms (Pure DPPC bilayer with 128 lipids and 3655 water molecules)
> 
>  plz tell me wht  can i do , to overcome that error.
> 
> 
> 
> > Hi Alok,
> >                 You need to add new topologies at ff???.rtp file, add
> > the name of your residue at aminoacid.dat file and save it in a folder
> with all changed files. **(((Follow the HEME example present at
> > ffgmx.rtp file)))**.
> >
> > --
> >                       Arlan da Silva Gonçalves
> >                IME(Instituto Militar de Engenharia)
> >                 Departamento de Engenharia Química
> >                  Pça. General Tibúrcio, 80 - Urca
> >                  22290-270 - Rio de Janeiro - RJ
> >                       Tel. (0xx21) 2546-7057
> >                       Fax. (0xx21) 2546-7059
> >
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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://xray.bmc.uu.se/~spoel
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