Hi
I don't know much about QM code so I leave this issue to QM experts.
cheers.
Hai
On Wed, Jan 18, 2017 at 5:20 PM, Aseel Bala <balaahme.msu.edu> wrote:
> Thanks so much for the clarification.
>
> When I use parmed, 156 atoms are identified to fulfill the qmmask - this
> sounds about right.
>
>
>
> Is it possible that the problem lies in the cutoff region I have selected
> for the qm region (using cut and qmcut)?
>
> I am seeing two things in the qmtry.out file from sander that are strange:
>
>
>
> 1. Line 92: says Mask :16 <:3.0; matches 4530 atoms.
>
> 2. The bottom says "QM region + cutoff larger than box. Cannot
> continue, need larger box". I doubt that the region is actually larger than
> the box because even when I reduce the qmmask to take atoms within 1
> angstrom and make the cutoff 2.0 angstroms in a box that is roughly
> 35x35x35
> Angstroms, I get the same error.
>
>
>
> Any ideas as to what is going on? I attached the input and output files
> here.
>
>
>
> Thanks,
>
> Aseel
>
>
>
> -----Original Message-----
> From: Hai Nguyen [mailto:nhai.qn.gmail.com]
> Sent: Wednesday, January 18, 2017 3:59 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] ambmask issue
>
>
>
> oops, sorry to mention that this is python code.
>
>
>
> So either
>
>
>
> - Use ipython and then type each command for interactive coding or create a
> file named "my.py" (or so on) then python my.py
>
>
>
> cat > my.py <<EOF
>
>
>
> import parmed as pmd
>
>
>
> qmmask='(:16 <:3.0)'
>
>
>
> parm = pmd.load_file('simbox.prmtop', xyz='c16.inpcrd') # replace ala3_solv
> by your real system name
>
>
>
> print(parm[qmmask])
>
> EOF
>
>
>
> python my.py
>
>
>
> Hai
>
>
>
> On Wed, Jan 18, 2017 at 3:53 PM, Aseel Bala < <mailto:balaahme.msu.edu>
> balaahme.msu.edu> wrote:
>
>
>
> > Hi,
>
> >
>
> >
>
> >
>
> > I am having a little bit of trouble with how to import parmed as pmd.
>
> > Do I just put the following lines into the command line:
>
> >
>
> >
>
> >
>
> > import parmed as pmd
>
> >
>
> > qmmask='(:16 <:3.0)'
>
> >
>
> > parm = pmd.load_file('simbox.prmtop', xyz='c16.inpcrd') # replace
>
> > ala3_solv by your real system name
>
> >
>
> > print(parm[qmmask])
>
> >
>
> >
>
> >
>
> > When I do this, I get an error in line 4 that says
>
> >
>
> >
>
> >
>
> > -bash: syntax error near unexpected token `('
>
> >
>
> >
>
> >
>
> > Is there something wrong with the syntax or should I be importing
>
> > parmed a different way?
>
> >
>
> > Also, when I type in the first line, it takes a long time for me to
>
> > get the '$' indicating that I can enter my next command.
>
> >
>
> >
>
> >
>
> > Thanks,
>
> >
>
> > Aseel
>
> >
>
> >
>
> >
>
> >
>
> >
>
> > -----Original Message-----
>
> >
>
> > From: Hai Nguyen [ <mailto:nhai.qn.gmail.com> mailto:nhai.qn.gmail.com]
>
> >
>
> > Sent: Tuesday, January 17, 2017 2:15 PM
>
> >
>
> > To: AMBER Mailing List < <mailto:amber.ambermd.org> amber.ambermd.org>
>
> >
>
> > Subject: Re: [AMBER] ambmask issue
>
> >
>
> >
>
> >
>
> > Cross testing: Can you use ParmEd to test the mask to make sure two
>
> > programs (parmed and sander) produce the same n_atoms?
>
> >
>
> >
>
> >
>
> > import parmed as pmd
>
> >
>
> > qmmask='(:16 <:3.0)'
>
> >
>
> >
>
> >
>
> > parm = pmd.load_file('ala3_solv.parm7', xyz='ala3_solv.rst7') #
>
> > replace ala3_solv by your real system name
>
> >
>
> > print(parm[qmmask])
>
> >
>
> >
>
> >
>
> > Hai
>
> >
>
> >
>
> >
>
> > On Mon, Jan 16, 2017 at 4:50 PM, Aseel Bala < <mailto:balaahme.msu.edu>
> balaahme.msu.edu> wrote:
>
> >
>
> >
>
> >
>
> > > Hi everyone,
>
> >
>
> > >
>
> >
>
> > > I still have not be able to find an answer to the question below. I
>
> > > am
>
> >
>
> > > thinking that this may be a bug in amber.
>
> >
>
> > >
>
> >
>
> > > Now, I am interested in looking at the codes within sander that
>
> >
>
> > > calculate atom or residue selections through the ambmask.
>
> >
>
> > >
>
> >
>
> > > Does anyone know which subroutine(s) within sander carries these
>
> >
>
> > > operations out so I know where to start looking?
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > Thanks,
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > --
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > Aseel Bala Ahmed
>
> >
>
> > >
>
> >
>
> > > PhD Candidate, Chemical Engineering
>
> >
>
> > >
>
> >
>
> > > Michigan State University
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > -----Original Message-----
>
> >
>
> > > From: Aseel Bala <balaahme.msu.edu>
>
> >
>
> > >
>
> >
>
> > > Date: Thu, 17 Nov 2016 13:21:11 -0500
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > Hi everyone,
>
> >
>
> > >
>
> >
>
> > > I am trying to select all molecules within 3 angstroms of a
>
> >
>
> > > residue(in this
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > case residue 16) using a mask.
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > I centered residue 16 in the middle of a 40x40x40 A box. Therefore I
>
> >
>
> > > know
>
> >
>
> > >
>
> >
>
> > > that there is plenty of space around it before I hit a boundary.
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > I have tried the syntax: qmmask='(:16 <:3.0)'
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > To select all residues within 3 A of residue 16 but to no avail. For
>
> >
>
> > > some
>
> >
>
> > >
>
> >
>
> > > reason, it tells me that the mask matches all the atoms in the box.
>
> > > It
>
> >
>
> > > gives
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > me the same error when I choose even 1 A instead of 3.
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > Is there a problem with how I am writing the ambmask?
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > >
>
> >
>
> > > Thanks in advance,
>
> >
>
> > >
>
> >
>
> > > --
>
> >
>
> > >
>
> >
>
> > > Aseel Bala
>
> >
>
> > >
>
> >
>
> > > Michigan State University
>
> >
>
> > >
>
> >
>
> > > _______________________________________________
>
> >
>
> > >
>
> >
>
> > > AMBER mailing list
>
> >
>
> > >
>
> >
>
> > > AMBER.ambermd.org
>
> >
>
> > >
>
> >
>
> > > <http://lists.ambermd.org/mailman/listinfo/amber>
> http://lists.ambermd.org/mailman/listinfo/amber
>
> >
>
> > >
>
> >
>
> > > _______________________________________________
>
> >
>
> > > AMBER mailing list
>
> >
>
> > > <mailto:AMBER.ambermd.org> AMBER.ambermd.org
>
> >
>
> > > <http://lists.ambermd.org/mailman/listinfo/amber>
> http://lists.ambermd.org/mailman/listinfo/amber
>
> >
>
> > >
>
> >
>
> > _______________________________________________
>
> >
>
> > AMBER mailing list
>
> >
>
> > <mailto:AMBER.ambermd.org> AMBER.ambermd.org
>
> >
>
> > <http://lists.ambermd.org/mailman/listinfo/amber>
> http://lists.ambermd.org/mailman/listinfo/amber
>
> >
>
> > _______________________________________________
>
> > AMBER mailing list
>
> > <mailto:AMBER.ambermd.org> AMBER.ambermd.org
>
> > <http://lists.ambermd.org/mailman/listinfo/amber>
> http://lists.ambermd.org/mailman/listinfo/amber
>
> >
>
> _______________________________________________
>
> AMBER mailing list
>
> <mailto:AMBER.ambermd.org> AMBER.ambermd.org
>
> <http://lists.ambermd.org/mailman/listinfo/amber>
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 18 2017 - 14:30:05 PST
