[gmx-users] How to create three different zones to minimize energy of a enzyme?

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 19 01:51:13 CET 2008

Evanildo Júnior wrote:
> Dear gmx-users,
> I would like to minimize the potential energy of the active site of an 
> enzyme. Because I do not have too much computer power to perform a full 
> enzyme calculation, I need to create three different zones in which the 
> calculation will take place. The first one is  the outer boundary of the 
> enzyme that will remain frozen during the calculation.

Look for "freeze groups" in the manual. They work with MD and I'm 
guessing they also work with EM.

> The second one is 
> a transition region between the active site region and the outer 
> boundary, whose atoms will receive a parabolic potential in order to 
> move just a little bit. 

Use position restraints.

> The last one is the active site itself which 
> will be freely minimized. I would like to know how do I implement it in 
> practice. Does anyone has a Gromacs script for this task? The other 
> question is how do I freeze only the C-alpha chain?

Apply a freeze group only to the C-alpha atoms. You'll need to use 
make_ndx to make the group and give that index file to grompp as well as 
the usual stuff.

If you're as new to GROMACS as you sound like you might be, you should 
do some tutorial material and read the first few chapters of the manual 
thoroughly. Doing the above would not be a good way to get your first 
exposure to using GROMACS.


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