[gmx-users] doesn't match coordinate file with topology

Peyman Yamin Peyman.Yamin at cbi.uni-erlangen.de
Thu Jul 24 12:40:04 CEST 2008

On Thursday 24 July 2008 09:46, minnale wrote:
> Hi users,
>      I have generated .gro file of protein by using .xtc file with trjconv
> command after that i used pdb2gmx command for generating topology file
> without any error. when I have inserted this protein into popc bilayer by
> using genbox command i has deleted some of the water and popc molecules,
> these residues i have mentioned in .top file but when i have used grompp
> command its showing that Fatal error:
>  Program grompp, VERSION 3.3.1
> Source code file: grompp.c, line: 448
> Fatal error:
> number of coordinates in coordinate file (2hel_popc7.6.gro, 12882)
>              does not match topology (2hel_noH1.top, 12832)
> The same system which is protonated state of protein simulating without
> generated .gro file by using trjconv command its running fine, But above
> mentioned system (unprotonated state) showing some fatal error
> Couls you pls tell me some suggestion.
> Thanks in advance

[ atoms ] section of the topology file lists and enumerates the atoms of your 
molecule. this should correspond to that from the .gro file of the molecule. 
in [ molecules ] part of the topology the number of the molecules should be 
mentioned correctly.

if you delete things from coordinate file, you should apply the proper change 
to the topology as well.

it seems you have more atoms in your gro than what is expected from the 
topology file. might want to find out why :)


Peyman Yamin
Lehrstuhl fuer Thermische Verfahrenstechnik
Universitaet Erlangen-Nuernberg
Egerlandstr. 3
91058 Erlangen
Phone: +49(0) - 9131 - 85 27671
Mailto: peyman.yamin at cbi.uni-erlangen.de

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