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Insert TM segments to membrane
- Justin
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13 years 10 months ago #377
by Justin
Insert TM segments to membrane was created by Justin
Dear all,
I have carefully read the tutorials and inserted the proteins into POPE membrane using the following command: genbox -cp protein.gro -cs pope.gro -o protein_lipid.gro -vdwd 0.24.
Before doing this, I centered the coarse grained protein in the box with the same dimension as that of the POPE bilayer cell. The tool I used is editconf with flags like "-c -box -princ".
Did I do the right way? I am not sure with my method.
Another question is why the van der Waals diameter is suggested to increase to 0.24.
Thanks!
I have carefully read the tutorials and inserted the proteins into POPE membrane using the following command: genbox -cp protein.gro -cs pope.gro -o protein_lipid.gro -vdwd 0.24.
Before doing this, I centered the coarse grained protein in the box with the same dimension as that of the POPE bilayer cell. The tool I used is editconf with flags like "-c -box -princ".
Did I do the right way? I am not sure with my method.
Another question is why the van der Waals diameter is suggested to increase to 0.24.
Thanks!
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- durbignon
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13 years 10 months ago #378
by durbignon
Replied by durbignon on topic Insert TM segments to membrane
Hi Justin,
Centering the protein before inserting into the membrane is definitely fine! Make sure it is correctly oriented wrt the membrane.
And the vdwd is increased since the coarse-grain bead does have a larger radius compared to an atomistic particle.
Centering the protein before inserting into the membrane is definitely fine! Make sure it is correctly oriented wrt the membrane.
And the vdwd is increased since the coarse-grain bead does have a larger radius compared to an atomistic particle.
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