Re: AMBER: How to build a cubic box of a newly synthesized compound?

From: M. L. Dodson <>
Date: Wed, 24 Dec 2008 11:45:23 -0600

On Wed, Dec 24, 2008 at 02:34:13PM +0800, Jeffrey wrote:
> Dear all,
> I'd like to perform a md simulation of a newly synthesized compound to calculate the dielectric constant. But before the md is carried out, a cubic box of the compound should be built with a reasonable density. But I don't know how to place the molecules in the box, such as orientation, relative position etc. Could someone please give me suggestions on how to do it conveniently?
> Thanks very much for the time.
> Happy Christmas day.
> ----
> Jeffrey

Look at
for some ideas.

You will, of course, have to create AMBER residue descriptors for your
new compound (see the antechamber module documentation and read the
archives of this email list).

After creating initial versions of the so-called prmtop and coord
files with xleap or tleap, you will have to run an initial constant
volume simulation to adjust the temperature followed by a constant
pressure simulation to adjust the density. Issues of orientation and
relative position will be sorted out in these equilibration runs. Do
not forget to image the system with ptraj at the end (or, instead, you
can just set iwrap=1 in the sander or pmemd input file, although this
might not be a good idea for production runs. I know diffusion
calculations are compromised by iwrap=1, but do not know about
dielectric constant calculations). When all the equilibration steps
are successfully completed, you will be ready for production MD runs.
One good way to check that your preparations went all right would be
to check for temperature drift in NVE production simulations.

Bud Dodson
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email:	mldodson-at-comcast-dot-net
Phone:	eight_three_two-56_three-386_one
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Fri Dec 26 2008 - 01:09:33 PST
Custom Search