(unknown charset) Re: [AMBER] Atom selection for restraints. .. .
"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.
At Tue, 30 Oct 2012 09:18:22 -0500,
Date, Mihir wrote:
> 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
> 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. .
> 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.:
> Hope this helps.
> 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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> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> (801) 587-9652
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Received on Tue Oct 30 2012 - 14:30:02 PDT