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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Received on Tue Oct 30 2012 - 08:00:03 PDT
