Re: AMBER: using LJ 10-12 non bonded potential for glycoproteins in Amber8

From: David A. Case <>
Date: Wed, 17 Mar 2004 11:26:00 -0800

On Wed, Mar 17, 2004, Tom Turner wrote:
> So, this I have done by including the -DHAS_10_12 flag in the
> AMBERBUILDFLAGS section of the config.h file. I can then successfully
> compile amber8 but running "make test" produces an error during the
> ./Run.tleap test - "Program error in leap". This error did not occur
> without the flag. Is this a bug?

First, you seem to have obtained some prelease form of Amber 8(?). We don't
have any way of knowing what version this is, or what bugs might be there.
You should order the official version, which is now released.

Second, since all you (should have) done is re-compile sander, it is hard
to see how this could have introduced a program error in leap. My guess is
that you will have to study your test cases more closely.

Third, you should probably consider using the real glycam04 force field,
which is included with Amber 8.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Wed Mar 17 2004 - 19:53:00 PST
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