[gmx-users] justin-lipid tutorial........

rama david ramadavidgroup at gmail.com
Tue May 8 14:06:41 CEST 2012

Hi gromac friends
I am performing the justin tutorials on lipids

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,
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