AMBER Archive (2007)

Subject: RE: AMBER: Restraintmask syntax

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Dec 05 2007 - 12:00:49 CST

Thanks for your lesson. I have started "heating", under the conditions of Amber
tutorial A3. It is going on fine, in particular the restraints have all been
accepted. This should prevent - I hope - the lipid molecules going too much
around.

francesco

--- Andrew Purkiss-Trew <a.purkiss_at_mail.cryst.bbk.ac.uk> wrote:

> On Tue, 2007-12-04 at 09:44 -0800, Francesco Pietra wrote:
> > --- Steve Spronk <spronk_at_umich.edu> wrote:
> >
> > The mask that you'll need to use is
> > >
> > > :77-521 | :POP_at_O2,P1,O3,O4,O1,C15,C11,N,C12,C13,C14
> > >
> > > Note the syntax of this mask. If I understand your system correctly, in
> > > your sample mask, you used the "and" character ("&") when you probably
> meant
> > > the "or" character ("|").
> >
> > I want to restraint protein, ligand, and that part of the lipid membrane.
> > Therefore, it should be "&", if the common meaning of "or" applies.
> >
>
> You do need the "or" operator. The mask works by combining the bits you
> specified logically. Think of each section of the mask as a mask of its
> own and then consider how the operator ("and","or" or "not") will
> combine the separate 'submasks'.
>
> So, from the example above
>
> :77-521 | :POP_at_O2,P1,O3,O4,O1,C15,C11,N,C12,C13,C14
>
> means include atoms that are in residues 77-521 or atoms that are in the
> list from the residue type POP. So there are two groups and you want all
> of the atoms in the first 'submask' or in the second 'submask'
>
> if you have
>
> :77-521 & :POP_at_O2,P1,O3,O4,O1,C15,C11,N,C12,C13,C14
>
> it would match atoms that are in residues 77-521 and are also in the
> list of atoms in the POP residue types. Again there are two groups and
> you would get all of the atoms that are in the first 'submask' AND in
> the second 'submask'. So unless any of residues 77 to 521 are also a
> POP, no atoms will match.
>
> You should use the ambmask program to see that list of atoms that a mask
> matches and you should see the difference clearly. Look at section 13.5
> of the amber 9 manual for details.
>
> Hope that this help explain things.
>
> > >
> > > ":POP, 77-521 & @%O2, P1, O3, O4, O1, C15, C11, N, C12, H21, H22, H23,
> C13,
> > > H31, H32, H33, C14, H41, H42, H43, H11, H12, H51, H52"
> > >
> > > Any trick to account for the polar head of POPC? Thanks for help
> > >
>
>
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