Re: [AMBER] How to choose a particular region to minimization?

From: Marc van der Kamp <>
Date: Fri, 31 Aug 2012 11:49:06 +0100

There are 2 simple options to fix/restrain atoms to their original
positions, ibelly and ntr=1 (Read the appropriate section in the manual,
section 2.5.4 in the AMBER12 manual) .
Personally, I prefer the ntr=1 option.

Both require a mask to indicate which atoms you want to fix/restrain. This
mask will have explicit residue numbers/atoms. So you first need to work
out which residues are within 5A from your ligand; there are many ways to
do this. One option would be to use VMD (if you are familiar with it) - the
benefit here is that you can use the 'byres' and 'within' selection
keywords to select all residues that have at least one atom within 5A of
your ligand. Once you've got a list of residues that have atoms within 5A
of your ligand, you can use this to set up your mask, e.g.:


Where residues 1, 3, 4 and 5 would be free to move (i.e. the residues with
atoms within 5A of your ligand).

If you set restraint_wt to 100 or so, you will effectively keep all atoms
that are in residues further than 5A from your ligand in their original
positions (defined by the refc coordinates).

Hope this helps - be sure to read the manual carefully and if you have
questions about selections in VMD, you can try their mailing list.

Good luck,

On 31 August 2012 07:55, Thanh Binh NGUYEN <>wrote:

> Dear AMBER user,
> I want to run a minimization for protein-ligand complex, but I want
> the region within 5A from ligand are moving, all the remaining part
> are fixed. What should I add in the *.in file to do that? (PS: I found
> "cap" command but it's only for water)
> Thanks in advance.
> Nguyen T.B.
> PhD student, Bioinformatics institute, Singapore
> _______________________________________________
> AMBER mailing list
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Received on Fri Aug 31 2012 - 04:00:04 PDT
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