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<BR>
<BR>
Thank you Peyman<BR>
<BR>
On Thu, 24 Jul 2008 Peyman Yamin wrote :<BR>
>On Thursday 24 July 2008 09:46, minnale wrote:<BR>
> > Hi users,<BR>
> > I have generated .gro file of protein by using .xtc file with trjconv<BR>
> > command after that i used pdb2gmx command for generating topology file<BR>
> > without any error. when I have inserted this protein into popc bilayer by<BR>
> > using genbox command i has deleted some of the water and popc molecules,<BR>
> > these residues i have mentioned in .top file but when i have used grompp<BR>
> > command its showing that Fatal error:<BR>
> > Program grompp, VERSION 3.3.1<BR>
> > Source code file: grompp.c, line: 448<BR>
> ><BR>
> > Fatal error:<BR>
> > number of coordinates in coordinate file (2hel_popc7.6.gro, 12882)<BR>
> > does not match topology (2hel_noH1.top, 12832)<BR>
> ><BR>
> > The same system which is protonated state of protein simulating without<BR>
> > generated .gro file by using trjconv command its running fine, But above<BR>
> > mentioned system (unprotonated state) showing some fatal error<BR>
> ><BR>
> > Couls you pls tell me some suggestion.<BR>
> > Thanks in advance<BR>
><BR>
><BR>
>[ atoms ] section of the topology file lists and enumerates the atoms of your<BR>
>molecule. this should correspond to that from the .gro file of the molecule.<BR>
>in [ molecules ] part of the topology the number of the molecules should be<BR>
>mentioned correctly.<BR>
><BR>
>if you delete things from coordinate file, you should apply the proper change<BR>
>to the topology as well.<BR>
><BR>
>it seems you have more atoms in your gro than what is expected from the<BR>
>topology file. might want to find out why :)<BR>
><BR>
>Peyman<BR>
><BR>
><BR>
><BR>
><BR>
>--<BR>
>Peyman Yamin<BR>
>Lehrstuhl fuer Thermische Verfahrenstechnik<BR>
>Universitaet Erlangen-Nuernberg<BR>
>Egerlandstr. 3<BR>
>91058 Erlangen<BR>
>Phone: +49(0) - 9131 - 85 27671<BR>
>Mailto: peyman.yamin@cbi.uni-erlangen.de<BR>
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