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]
Sent: Tuesday, January 17, 2017 2:15 PM
To: AMBER Mailing List <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 <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
>
> _______________________________________________
>
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>
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>
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>
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Received on Wed Jan 18 2017 - 13:00:04 PST
