Hi gromac friends I am performing the justin tutorials on lipids http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials
I am strugling now on 3rd steps I have following queris regarding to steps ... 1. I increase the van der walls radii of carbon from the 0.15 to 0.375 > Is these also increases the vanderwall radii of protein ...?? If it increases the radii of protein , then how to add water in protein core ...??? 2. What is the meaning of continue to adjust the van der waals radius of carbon ??? Please comment in detail... 3. After solvation I given the following command to ion addition grompp -f ions.mdp -c solv.pdb -p topol.top -o ions.tpr I got following reply ... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8# Generated 837 of the 2346 non-bonded parameter combinations ------------------------------------------------------- Program grompp, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/grompp.c, line: 479 Fatal error: No molecules were defined in the system For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "Making merry out of nothing, like in refugee camp" (Gogol Bordello) Please give me some valuable suggestion Rama David... With Best Wishes,
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists