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

From: Thanh Binh NGUYEN <>
Date: Fri, 31 Aug 2012 19:09:50 +0800

Thank Marc very much for your clear explanation. I will apply it to my
work now.
Nguyen T.B.
PhD student, Bioinformatics institute, Singapore

Quoting Marc van der Kamp <>:
> 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.:
> restraintmask='!:1,3-5'
> 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,
> Marc
> 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 - 04:30:02 PDT
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