RE: AMBER: RE:Amber 8 with lam compilation problem

From: Ross Walker <>
Date: Wed, 23 Feb 2005 10:02:47 -0800

> Thx very much it is working :) . I understand that i must have 2
> ambers on
> my computers when i want run seriall jobs and somtimes run
> parallel , but i
> must have two different AMBERHOME variables. How to solve this
> not setting
> it always when i want to run seriall ? . Can i add somehow AMBERHOME2
> variable ?

You don't actually need $AMBERHOME set to run sander. It is only actually
required for Leap. I just use it in my examples as a kind of generic amber
path. If you use the full path in your scripts (always a good idea in my
opinion) then you won't have any problems. Alternatively you could just copy
the parallel sander and sander.LES executables out of the parallel
compilation directory and put them in the serial directory called sander.mpi
and sander.LES.mpi or something similar. Then just remember to use these
names instead of just sander when running in parallel.

> Is it possible to compile pmemd with intel fortran 8.1 compiler
> ?? becouse i
> cant configure it .

Yes, although you need a special configure script. There is a note posted on
the archive somewhere about it. Check
There may also be something on the amber website about it but I forget
where. If you can't find it in the archive or on the website post a message
to the mailing list again and Bob Duke will probably help you out.
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 Wed Feb 23 2005 - 18:53:02 PST
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