One thing that may help is that the mask syntax actually allows for
distance-based criteria. So for instance, to select all residues within
4.5 Angstroms of residue 5, you would do something like this:
(:5 <. 4.5)
This is described in the "ambmask" section of the Amber 12 reference manual.
HTH,
Jason
On Fri, Aug 31, 2012 at 7:09 AM, Thanh Binh NGUYEN <
nguyentb.bii.a-star.edu.sg> wrote:
> 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 <marcvanderkamp.gmail.com>:
> > 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 <nguyentb.bii.a-star.edu.sg
> >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
> >>
> >>
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> >>
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> >
> >
>
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Aug 31 2012 - 08:00:04 PDT
