Re: [AMBER] How can I run Production MD for lipid in Amber12 using Lipid11-ff?

From: Jason Swails <>
Date: Tue, 23 Sep 2014 08:04:53 -0400

On Tue, 2014-09-23 at 20:44 +0900, Bikash Ranjan Sahoo wrote:
> Dear Dr Hannes and Dr. David,
> I do not have Amber14 license. I cannot install Amber14 tools in
> parallel or serial in my cluster also. Tried many times and failed.

I am surprised you had problems. In my experience, the commands

./configure gnu
make install

are enough to get AmberTools 14 installed on any system that is properly
set up (i.e., has the relatively small number of necessary prerequisites
-- see and for
example). If you cannot get it installed, google the error messages you
receive (or, if the error messages are helpful, follow their advice).
If you are still having problems, ask here.

> Will
> you be kind enough to share a useful tutorial to simulate a lipid and
> protein in bilayer using Lipid11-ff.

See the advanced tutorial 16.

It used to be for Lipid11 before it was updated to Lipid14. Using both
force fields is effectively the same. However, Lipid14 is _so_ much
better than Lipid11 that there is no justifiable excuse for using
Lipid11 for production simulation (unless you are doing some type of
comparison study). Any reviewer with knowledge in the area of lipid
simulations will tell you to go back and use a better force field.

> Upto Holding production run, pmemd.MPI
> is running perfectly. Only production MD is not running and giving these
> errors as mentioned in my earlier email. Kindly help me in solving this
> problem for which I shall remain ever grateful to you.

Pay careful attention to the error messages you receive. The last one
you reported was:

amber-dopg-chl> forrtl: severe (19): invalid reference to variable in
NAMELIST input, unit 5, file
amber-dopg-chl/, line 23, position 10

So, look at the 10th character on line 23 of your file.
Either you are using a variable that is not part of that namelist or you
made a typo. (like nbt instead of ntb or something).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 23 2014 - 05:30:03 PDT
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