<div class="gmail_quote"><div>By hand is the easiest way.<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
</div>Ya, sorry I wrote it wrong.But why these extra atoms are present in my<br>
topology file and how to correct it.<br>
<br>
Thanks,<br>
<br>
Regards,<br>
Swati<br>
<div><div></div><div class="h5"><br>
><br>
> On Thu, Jul 16, 2009 at 12:36 PM, <<a href="mailto:swatik@ncbs.res.in">swatik@ncbs.res.in</a>> wrote:<br>
><br>
>> Hi,<br>
>><br>
>> thanks for your reply.<br>
>><br>
>> Yes their is difference of 5 solvent molecules. They are more in number<br>
>> in<br>
>> my topology file.<br>
>><br>
>> Regards,<br>
>> Swati<br>
>><br>
>> >><br>
>> >><br>
>> >> I am running simulation for the drug enzyme complex using Gromacs<br>
>> with<br>
>> >> gromacs96(43a2)forcefield. After generating waterbox around my<br>
>> protein,<br>
>> >> when I am running grompp command (before energy minimization) I am<br>
>> >> getting<br>
>> >> following error:<br>
>> >><br>
>> >><br>
>> ---------------------------------------------------------------------------<br>
>> >> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#<br>
>> >> checking input for internal consistency...<br>
>> >> calling /lib/cpp...<br>
>> >> processing topology...<br>
>> >> Generated 380 of the 1326 non-bonded parameter combinations<br>
>> >> Excluding 3 bonded neighbours for Protein_A 1<br>
>> >> Excluding 2 bonded neighbours for SOL 735<br>
>> >> Excluding 3 bonded neighbours for ZPR 1<br>
>> >> Excluding 2 bonded neighbours for SOL 36755<br>
>> >> NOTE:<br>
>> >> System has non-zero total charge: -1.999999e+01<br>
>> >><br>
>> >> processing coordinates...<br>
>> >><br>
>> --------------------------------------------------------------------------<br>
>> >> Program grompp_mpi, VERSION 3.3.1<br>
>> >> Source code file: grompp.c, line: 448<br>
>> >><br>
>> >> Fatal error:<br>
>> >> number of coordinates in coordinate file (protein_gen.pdb, 119825)<br>
>> >> does not match topology (topology.top, 119830)<br>
>> >><br>
>> --------------------------------------------------------------------------<br>
>> >><br>
>> >> I checked gromacs wiki page<br>
>> >> also(<br>
>> >><br>
>> <a href="http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology" target="_blank">http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology</a><br>
>> >> )<br>
>> >> but not able to solve this error.I am getting this error before<br>
>> adding<br>
>> >> ions.<br>
>> >><br>
>> >> Can anybody help me regarding same and suggest what could be possible<br>
>> >> reason for this ?<br>
>> >><br>
>> >> Thanks,<br>
>> >><br>
>> >> Regards,<br>
>> >><br>
>> ><br>
>> ><br>
>> > I guess you just missed five atoms in your gro file. Does the number<br>
>> of<br>
>> > solvent molecules in the coordinate file equal to that in the<br>
>> topology?<br>
>> ><br>
>> > ~ Vitaly<br>
>> ><br>
>> ><br>
>> > --<br>
>> > Vitaly V. Chaban, Ph.D. (ABD)<br>
>> > School of Chemistry<br>
>> > V.N. Karazin Kharkiv National University<br>
>> > Svoboda sq.,4, Kharkiv 61077, Ukraine<br>
>> > email: <a href="mailto:chaban@univer.kharkov.ua">chaban@univer.kharkov.ua</a>,<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a><br>
>> > skype: vvchaban, mob.: +38-097-8259698<br>
>><br></div></div></blockquote></div>