Re: [AMBER] ambmask issue

From: Aseel Bala <balaahme.msu.edu>
Date: Wed, 18 Jan 2017 15:53:44 -0500

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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>

> AMBER.ambermd.org

>

> http://lists.ambermd.org/mailman/listinfo/amber

>

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Received on Wed Jan 18 2017 - 13:00:04 PST
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