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

Justin A. Lemkul jalemkul at vt.edu
Tue May 8 14:10:48 CEST 2012

On 5/8/12 8:06 AM, rama david wrote:
> 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 ...???

It will affect all carbon atoms.  If you need to do something more specialized, 
you'll probably have to use a different approach.  The above suggestion is to 
eliminate water from being placed within the lipid membrane.

>   2. What is the meaning of continue to adjust the van der waals radius of
> carbon ???
>       Please comment in detail...

"Continue to adjust" = change the value until you get satisfactory results.  The 
value of 0.375 generally works well for me, but some lipids pack differently and 
thus you may need to use a different value.  For the tutorial, which uses DPPC, 
0.375 should work fine.

>   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)

Somehow you've badly broken the topology.  At this point, it's hard to say how.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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