# [AMBER] Defining the box dimensions while making the top and crd files

From: Iqbal, Muhammad Sajid <iqbal.uleth.ca>
Date: Fri, 26 Jun 2015 12:48:46 -0600

Hi amber community,

Sorry for repeating the question. However, the recommended solutions for my
question did not work for me. I am providing more details here on what I
would like to do while defining the box space. I have a pdb file of my
simulation box and I determine the minimum and maximum coordinates of the
box in VMD using the following commands with box coordinates output.

*set all [atomselect top all]measure minmax \$all*
min = {-150.04800415039063 -150.0030059814453 -150.08200073242188}
max = {150.0 150.00100708007813 150.0}

My question was how I can use exactly min and max coordinates for top and
crd file formation? In standard procedure, we use the sum of min and max
coordinates if I am not wrong.

*set mypdb box {300.05 300.0 300.08}*

However, I could not get the right values after running the pre-MD
minimization step. After performing minimization step, my pdb file
coordinates are look like this which is quite different. I also tried with
setBox command but no luck.

min = {0.25999999046325684 0.3889999985694885 0.054999999701976776}
max = {300.65899658203125 300.7090148925781 300.6400146484375}

For my previous question, there were answers to define the box space along
with angles. I am sorry if I could not follow it right way.

I will be thankful if someone let me what exact command i need to write to
define the proper box space?

Regards,

" My previous question was;

Usually the box is defined using the combined vector values. How I can use
the minimum and maximum coordinates to define the box? i have the
coordinates as follows,

maximum = {150.0 150.2343 150.22}
minimum={-150.6945 -150.0 -150.34442}
combined= {300.6945 300.2343 300.56442}

mypdb = loadpdb mypdb.pdb
set mypdb box {-150.6945 -150.0 -150.34442} {150.0 150.2343 150.22}
"

------------------------------

Message: 30
Date: Thu, 25 Jun 2015 09:39:03 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] Defining the box dimensions while making the top
and crd files
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAEk9e3o2h4_SKS5+BXmMKZkHnRXKTnJXqfGifB3aHHjLkmfeBA.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

On Wed, Jun 24, 2015 at 8:02 PM, Iqbal, Muhammad Sajid <iqbal.uleth.ca>
wrote:

> Hi Amber folks,
>
> Usually the box is defined using the combined vector values. How I can use
> the minimum and maximum coordinates to define the box? i have the
> coordinates as follows,
>
> maximum = {150.0 150.2343 150.22}
> minimum={-150.6945 -150.0 -150.34442}
> combined= {300.6945 300.2343 300.56442}
>
>
> mypdb = loadpdb mypdb.pdb
> set mypdb box {-150.6945 -150.0 -150.34442} {150.0 150.2343 150.22}
>

?The box is defined as 3 lengths and 3 angles. So the syntax *should* be
something like this:

mypdb = loadpdb mypdb.pdb
set mypdb box {300.6945 300.2343 300.56442 90 90 90}

HTH,
Jason

```--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
Message: 31
Date: Thu, 25 Jun 2015 10:14:17 -0400
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] Defining the box dimensions while making the top
and crd files
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20150625141417.GA17981.scarletmail.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Thu, Jun 25, 2015, Jason Swails wrote:
> The box is defined as 3 lengths and 3 angles.  So the syntax *should* be
> something like this:
>
> mypdb = loadpdb mypdb.pdb
> set mypdb box {300.6945 300.2343 300.56442 90 90 90}
Just to avoid any confusion: what you see above is *not* the current syntax
in
tleap; this may change in a future revision.
For now, use the "set <unit> box" command in tleap to set the lengths (this
also sets the ifbox flag to indicate the presence of periodic boundary
conditions); then use the "ChBox" routine to change the angles if they are
not
all 90.
...dac
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```
Received on Fri Jun 26 2015 - 12:00:03 PDT
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