<br><br><div><span class="gmail_quote">On 8/15/07, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
vinod kumar wrote:<br>> Hi, gmx-users,<br>><br>> HI , how to overcome this problem<br>> the output after grompp if em.mdp ............<br>>> fatal error : number of coordinates in coordinate file ( solvated.gro
8655)<br>>> does not match topology ( top.top 8657)<br>><br>> i have made necessary changes in the .top file with respect to the out<br>> put of genbox .<br><br>It seems that you have either used a different .top file, or not changed
<br>it correctly. Go back a step and try again.<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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</a><br></blockquote></div><br>I sometimes have that problem when adding ligand with using Dundee server. <br>Checking the number of atoms in the .pdb(or .gro) file and its .itp file might be helpful. <br>When using Dundee server they give you the .gro file with all the hydrogen bound.
<br>But they give you 3 .pdb file. <br><br>-- <br>--------------------------------------------------<br>'God used beautiful mathematics in creating the world.'<br>-Paul Dirac <br>'But he created too many object.'
<br>-Seungpyo Hong <br><br>Seungpyo Hong <br>Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea<br>Tel. (82)-18-372-2468<br><a href="mailto:sphong_@kaist.ac.kr">sphong_@kaist.ac.kr</a><br><a href="mailto:sp1020@gmail.com">
sp1020@gmail.com</a>