RE: AMBER: wierd behavior of addions

From: Ross Walker <>
Date: Tue, 22 Mar 2005 11:45:32 -0800

> protein and the ions are actually in one line. I did several
> times and all
> get the same wierd behavior. Is this normal? Could anyone
> please explain
> why this is happening?

This is not normal. It is possible that it is the same / similar bug to the
problems seen with solvation in Leap. Unfortunately to date we have not been
able to track down the bug, it only occurs on some machines with certain
specific compilers etc. I know the portland group compilers have problems
with Leap so avoid these if you can. Leap should compile with gcc.

As a test skip the charge neutralisation stage and try solvating your system
and see if you get weird behaviour here as well.

If you can let us know what system you are running on it may help in
tracking down the problems. We need to know, Operating system, compilers,
compiler versions, processors, amber version, what bug fixes have been
applied etc.

Also, try recompiling your amber installation from scratch (make sure you do
a make clean in $AMBERHOME/src) and see if the problem still occurs. Run the
test cases and see which ones fail as well.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Tue Mar 22 2005 - 19:53:00 PST
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