Just FYI: if you want to look at the code
check $AMBERHOME/AmberTools/src/sqm/findmask.F90
(and grep qmmask *)
good luck.
Hai
On Wed, Jan 18, 2017 at 5:23 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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
>>
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>>
>> > <http://lists.ambermd.org/mailman/listinfo/amber>
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> >
>>
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>>
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>>
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>>
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Received on Wed Jan 18 2017 - 15:00:03 PST
