Hi GROMACS users,<br>sorry please disregard the earlier message realised it was too long.<br>i am new to GROMACS. i have been trying to run the Villin Benchmarks using the conf.gro, grompp.mdp and topol.top file provided with the benchmark folder. i giving the grompp command as follows
<br><br><span style="font-style: italic; font-weight: bold;">grompp -f grompp.mdp -c conf.pdb -p topol.top -o em.tpr</span><br style="font-style: italic; font-weight: bold;"><br>and after that i get this message,<br><br><span style="font-weight: bold; font-style: italic;">
Fatal error:</span><br style="font-weight: bold; font-style: italic;"><span style="font-weight: bold; font-style: italic;">number of coordinates in coordinate file (conf.pdb , 9389)</span><br style="font-weight: bold; font-style: italic;">
<span style="font-weight: bold; font-style: italic;"> does not match topology (topol.top, 0)</span><br style="font-weight: bold; font-style: italic;"><span style="font-weight: bold; font-style: italic;">-------------------------------------------------------
</span><br style="font-weight: bold; font-style: italic;"><br style="font-weight: bold; font-style: italic;"><span style="font-weight: bold; font-style: italic;">"The Candlelight Was Just Right" (Beastie Boys)</span>
<br><br>After going through the GROMACS mailing list I realised this is a classical mistake which everyone makes. that's fine, but even after making the changes as pointed out by many users that check the number of atoms in
topol.top and conf.gro file i am still getting the same error.<br>i am providing in the email conf.gro and the topol.top file. can anyone of you plz suggest as to what is wrong. where i have to make the changes<br>inorder for me to run the
simulation.thanks.<br>the file are provided below.<br><br>Arindam Ganguly<br><br>conf.gro<br>VILLIN in water<br> 9389<br> 1MET N 1 2.185 2.903 2.012 -0.4460 -0.1439 0.3043<br><span style="font-weight: bold;">
last line of the conf.gro file</span><br>3036SOL HW2 9389 4.069 1.007 3.359 0.8423 -0.6670 -0.9379<br> 5.02729 4.73973 4.10445 0.00000 0.00000 1.67574 0.00000 -1.67574 2.36986<br><br><span style="font-weight: bold;">
topol.top file</span><br>[ system ]<br>; Name<br>VILLIN in water<br><br>[ molecules ]<br>; Compound #mols<br>Protein 390<br>SOL 8999<br><br><br><br>