Hi gromac friends <br>I am performing the justin tutorials on lipids<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials</a><br>
<br>I am strugling now on 3rd steps <br>I have following queris regarding to steps ...<br><br>1. I increase the van der walls radii of carbon from the 0.15 to 0.375 <br> > Is these also increases the vanderwall radii of protein ...??<br>
If it increases the radii of protein , then how to add water in protein core ...???<br> <br> 2. What is the meaning of continue to adjust the van der waals radius of carbon ???<br> Please comment in detail...<br>
<br> 3. After solvation I given the following command to ion addition <br><br> grompp -f ions.mdp -c solv.pdb -p topol.top -o ions.tpr <br><br>I got following reply ...<br><br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#<br>
Generated 837 of the 2346 non-bonded parameter combinations<br><br>-------------------------------------------------------<br>Program grompp, VERSION 4.5.4<br>Source code file: /build/buildd/gromacs-4.5.4/src/kernel/grompp.c, line: 479<br>
<br>Fatal error:<br>No molecules were defined in the system<br>For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br><br>"Making merry out of nothing, like in refugee camp" (Gogol Bordello)<br><br><br><br><br>Please give me some valuable suggestion<br>Rama David...<br>
<br>With Best Wishes,<br>