(unknown charset) Re: [AMBER] Atom selection for restraints. .. .

From: (unknown charset) Bashford, Donald <Don.Bashford.stjude.org>
Date: Tue, 30 Oct 2012 16:07:50 -0500

Hi Mihir,

"Belly" is a different and nowadays little-used way of fixing
atom positions. Rather than using a restraining force, it sets a list
of atoms whose coordinates are never updated, regardless of
forces on them. So it's normal that the belly machinery stays off when
you specify restraints via restraintmask, etc.

-Don

At Tue, 30 Oct 2012 09:18:22 -0500,
Date, Mihir wrote:
>
> Hi
> Thanks a ton. It worked.
> With enclosure in single quotes I get restraint energy also notification of how many atoms are restrained
>
> 5. REFERENCE ATOM COORDINATES
>
> defa
> Mask !.H=; matches 2189 atoms
>
> Just out of curiosity though,
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 1
> restraint_wt = 500.00000
>
> ibelly is still zero before and after single quote enclosure. Is that ok?
>
> ________________________________________
> From: Daniel Roe [daniel.r.roe.gmail.com]
> Sent: Monday, October 29, 2012 6:10 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Atom selection for restraints. .
>
> Hi,
>
> Try enclosing the string in single quotes, and don't put any spaces.
> Also, I think it's enough to just specify no hydrogen atoms, e.g.:
>
> restraintmask='!.H='
>
> Hope this helps.
>
> -Dan
>
>
> On Mon, Oct 29, 2012 at 4:41 PM, Date, Mihir <Mihir.Date.stjude.org> wrote:
> > Hi
> > I want to restrain all atoms except hydrogen for my first minimization of protein and two ligands complex in vacuum.
> >
> > Following is my input for sander.
> >
> > &cntrl
> > imin = 1,
> > MAXCYC = 500
> > ncyc = 250,
> > ntb = 0,
> > igb = 0,
> > cut = 999,
> > ntr = 1,
> > restraint_wt=500.0,
> > restraintmask=:* & !.H=
> > /
> > END
> >
> > sander -O -i minimize.in -o mini_vaccu.out -p complex.prmtop -c complex.inpcrd -r complex_vaccu.rst -ref complex.inpcrd
> >
> > it gives me message
> >
> > Cannot match namelist object name .*
> > namelist not terminated with / or &end
> >
> > When I looked into output file, the restraints energy is 0.0000 and no atoms are selected for restraints.
> >
> > Frozen or restrained atoms:
> > ibelly = 0, ntr = 1
> > restraint_wt = 500.00000
> >
> > and in energy table
> > RESTRAINT = 0.0000
> >
> > The sytax I used for atom selection is exactly as shown in Amber12 manual (page 320). My input pdb has hydrogen present.
> > How I can select only heavy atoms and exclude all hydrogens from restraints?
> > Is there any mistake in my syntax for atom selection?
> >
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> >
> >
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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>
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Received on Tue Oct 30 2012 - 14:30:02 PDT
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