[gmx-users] make-hole,grasp

Chris Neale chris.neale at utoronto.ca
Mon Jun 25 16:23:06 CEST 2007

>Dear all
>I want to make hole in popc. i prepared the grasp
>molecular surface . how can i use grasp result in run

This sound like your previous message : http://www.gromacs.org/pipermail/gmx-users/2007-June/027994.html
And here is my previous answer : http://www.gromacs.org/pipermail/gmx-users/2007-June/028005.html

I continue to suggest that you read the make-hole manual, the location of which was specified in my previous message. 
The instructions are actually very well laid out. Also you should read the publication associated with the manual.
If you did indeed read the manual and the publication and can't understand what something means or perhaps you tried some
part and got an error message then be specific about that.

If you are finding make-hole too difficult, then you could do this instead:

1. determine the center of mass of your membrane in the z-dimension
2. use editconf to move your protein center of mass to approximately the same value in the z dimension
3. Make sure the membrane and the protein have the exact same size box
4. use genbox to solvate your protein with your membrane (genbox -cp protein.gro -cs membrane.gro)
5. energy minimize
6. put position restraints on the heavy atoms of your protein; put position restraints on the lipid P, but only in the Z dimension (N N Y)
7. Simulate for 10ns.
8. Release all of the position restraints
9. Simulate for 5ns.
10. Production dynamics

This method that I have outlined will not get you to equilibrium as quickly as will the make-hole program 
but the end result should be just as good. For a reasonably sized protein this entire process may take you a 2 weeks (parallel 4cpu) to two
months (1cpu). I don't recommend that you do this, I am just relating an alternative in case you can't make the make-hole program work. 
Another alternative is the inflategro program on Dr. Tieleman's website.


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