[gmx-users] Fatal error: number of coordinate file <cm5_b4ion.gro, 28016> does not match

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Wed Mar 23 17:35:02 CET 2005

> I have some problems with creation of my Drug-Enzyme complex  topology
> file. I-AEDANS acted as my Drug.
> The coordinate file of I-AEDANS was created by proDRG server.
> While using the instructions "Gromacs Tutorial for Drug-Enzyme Complex"
> written by John E. Kerrigan, Ph.D.
> IST/Academic Computing Services
> RWJMS-University of Medicine and Dentistry of NJ
> 675 Hoes Lane, RM SB11
> Piscataway, NJ 08854
> I've got DRGGMX.ITP and renamed it to iae.itp,
> then I used a program pdb2gmx for conversion of my enzyme cm5.pdb to
> cm5.gro The second step was to open DRGFIN.GRO in a text editor and paste
> all of the lines to CM5.GRO.
> Then:
> editconf -bt octahedron -f cm5.gro -o cm5.gro -c -d 1.0
> genbox -cp cm5.gro -cs spc216.gro -o cm5_b4ion.gro -p topol.top.
> grompp -f em.mdp -c cm5_b4ion.gro -p topol.top -o cm5_b4ion.trp.
> The last command is not proceded,
> exactly
> Fatal error: number of coordinate file <cm5_b4ion.gro, 28016> does not
> match tobology <topol.top, 0 >
>  Would you be able to help me with this problem?
>                                                                   Senserely
> yours Vladimir Schepanovsky.

Seems your top file got an error, check it if all itp files got loaded and if 
number of water is correct, take a look in the last line in the file perhaps 
there`s a missing newline.



 Florian Haberl                            Universitaet Erlangen/
 Computer-Chemie-Centrum    Nuernberg
                                                      Naegelsbachstr. 25
                                                      D-91052 Erlangen
  Mailto: florian.haberl AT chemie.uni-erlangen.de

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