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

[Justin A. Lemkul]

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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================