It seems atoms, not molecules... :)<br><br>~Vitaly<br><br><div class="gmail_quote">On Thu, Jul 16, 2009 at 12:36 PM, <span dir="ltr"><<a href="mailto:swatik@ncbs.res.in">swatik@ncbs.res.in</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
thanks for your reply.<br>
<br>
Yes their is difference of 5 solvent molecules. They are more in number in<br>
my topology file.<br>
<br>
Regards,<br>
Swati<br>
<div><div></div><div class="h5"><br>
>><br>
>><br>
>> I am running simulation for the drug enzyme complex using Gromacs with<br>
>> gromacs96(43a2)forcefield. After generating waterbox around my protein,<br>
>> when I am running grompp command (before energy minimization) I am<br>
>> getting<br>
>> following error:<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>
>> 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>
>> I checked gromacs wiki page<br>
>> also(<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 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 of<br>
> solvent molecules in the coordinate file equal to that in the 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>
<br>
<br>
</div></div></blockquote></div>