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

[minnale]

Thank you Peyman

On Thu, 24 Jul 2008 Peyman Yamin wrote :
>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
>
>
>
>
>--
>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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