[gmx-users] About Lipid Protein simualtion

[Justin Lemkul]

On 10/4/12 1:12 PM, vidhya sankar wrote:
> Dear Justin ,
>                       Thank you for you Previous reply.
>
>
> I am doing  Simulation of Cyclic Peptide in Lipids  I am following your tutorial  When I use inflategro script For my System I have got Output System_inflated.gro file with certain message in Command prompt as follows  . The Below Message Shows That There is No Lipid Molecules Are Deleted  Should I Change the Cut-off or scaling Factor  to Delete the Lipid Molecules or is it enough ,  I Mean  Must Some Lipid Molecules Need to be Deleted ?
>
>

It would be highly unusual if no lipids were deleted, unless the protein is not 
actually embedded in the membrane.

> There are 128 lipids...
> with 50 atoms per lipid..
> Determining upper and lower leaflet...
> 64 lipids in the upper...
> 64 lipids in the lower leaflet
> Centering protein....
> Checking for overlap....
> ...this might actually take a while....
> 100 % done...
> There are 0 lipids within cut-off range...
> 0 will be removed from the upper leaflet...
> 0 will be removed from the lower leaflet...
> Writing scaled bilayer & centered protein...
> Calculating Area per lipid...
> Protein X-min/max: 19    40
> Protein Y-min/max: 21    39
> X-range: 21 A    Y-range: 18 A
> Building 21 X 18 2D grid on protein coordinates...
> Calculating area occupied by protein..
> full TMD..
> upper TMD....
> lower TMD....
> Area per protein: 4 nm^2
> Area per lipid: 8.9375 nm^2
> Area per protein, upper half: 3.5 nm^2
> Area per lipid, upper leaflet : 8.9453125 nm^2
> Area per protein, lower half: 3.5 nm^2
> Area per lipid, lower leaflet : 8.9453125 nm^2
> Writing Area per lipid...
> Done!
>
> 2) Also When I Run Grompp for EM Which Topology Should  I use ?  I have  used my Multi chain     protein.top When I Have used that I got Error AS follows
> Fatal error:
>
> [ file strong_porse.itp, line 8 ]:
> Atom index (4) in position_restraints out of bounds (1-3).
> This probably means that you have inserted topology section "position_restraints"
> in a part belonging to a different molecule than you intended to.
> In that case move the "position_restraints" section to the right molecule.
> For more information and tips for troubleshooting, please check the GROMACS
>
> How to Rectify the Problem?

Position restraints can only be applied within a given [moleculetype].  Note 
that the error is explained on the Gromacs website, along with an example of 
proper usage:

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

-Justin

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

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