[gmx-users] About Lipid Protein simualtion
jalemkul at vt.edu
Thu Oct 4 19:20:46 CEST 2012
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...
> 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
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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