Re: [AMBER] is membrane protein simulation tutorial ready?

From: Jason Swails <>
Date: Sat, 21 Apr 2012 16:32:50 -0400

Given the interest, I'm guessing there will be an announcement when it is

Tutorials are difficult and time-consuming to put together, and they are
put together by volunteers that donate their time to do it (and it's only
been 10 days since you last asked).

In the meantime, I encourage you to experiment setting one up without an
official tutorial. There are no additional programs included with
AmberTools 12 (compared to AmberTools 1.5, anyway) that will aid in
building membrane systems. Therefore, tools useful in generating membrane
structures (e.g., those used in CHARMM and gromacs) will probably be useful
for Amber as well. The lipid force field libraries and force field
parameters (found in $AMBERHOME/dat/leap/lib and $AMBERHOME/dat/leap/parm)
will give you hints about the atom and residue naming that Amber expects.

There were also additional pressure scaling options made available
specifically designed to address membrane simulation needs--constant
surface tension and expanded non-isotropic pressure scaling options. These
are described in the manual, and there is an example at
$AMBERHOME/test/csurften with a sample chamber topology file (using the
CHARMM lipid force field). These demonstrate the input file parameters
needed to carry out these kinds of simulations.

Becoming familiar with the above should help you get through the tutorial
faster when it's released, too.

Good luck,

On Sat, Apr 21, 2012 at 3:14 PM, Albert <> wrote:

> Hello:
> I am wondering is the Amber membrane protein simulation tutorial
> ready? I am looking forward to that.
> thank you very much
> best
> Albert
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Sat Apr 21 2012 - 14:00:03 PDT
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