[gmx-users] problems in grompp

[Alok]

Thanks for ur reply :-)
problem was in my dppc128.pdb file actually it was not downloaded properly.
now it is going well. :-)
Thanks

> 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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