AMBER Archive (2007)

Subject: RE: AMBER: Restraintmask syntax

From: Andrew Purkiss-Trew (a.purkiss_at_mail.cryst.bbk.ac.uk)
Date: Wed Dec 05 2007 - 04:39:08 CST

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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