RE: AMBER: tleap load pdb file

From: Ross Walker <>
Date: Sun, 6 Feb 2005 10:50:29 -0800

Dear Xiaowen

> Your suggestions and ideas are really helpful to a new UNIX
> and amber user.

The errors you have been seeing with Xleap and tleap are really strange. The
really high residue number you are seeing is indicative of the sort of thing
that can happen when a variable is un-initialised, or if some pointer is
pointing to the wrong memory location. This will need more investigation to
fix as it is not just a simple pdb formatting issue. This is especially true
since the test cases fail.

A few things...

1) We need to get tleap working first of all. Until tleap is working there
is NO chance of xleap working so I wouldn't worry about xleap for the

2) tleap is completely txt based so it is definitely not an issue with
xwin32 etc...

One option may be that it is either a leap bug or a compiler bug... Which it
is I am not sure at the moment. I will need a lot information to work out
what the problem is. Can you please send me all of the specs of your
machine, operating system and version. Amber version + which bug fixes have
been applied. Compiler and version? E.g. xlf for fortran. Note xleap is
written in c so I need to know the c compiler and version as well. Is it

One other thing you can try... Create a new directory for amber. E.g.
Amber8_test and put a "fresh" copy of amber8 in that directory. From the
amber8 cd if you can. Then download bugfix.all from the amber website
( and apply it as per the

Then copy in the config.h file I have attached to this email into the src
directory of the new amber 8 installation. YOU WILL NEED TO MODIFY THE
AMBER8 INSTALLATION. I have assumed you have an AIX machine with the xlf

The cd to the src directory and do

make clean

This should hopefully build you a full amber installation. Then see if this
version of tleap and xleap works. Note the make file I have sent you has
optimisation turned off so don't use this installation for simulations (e.g.
avoid compute expensive code such as sander - use the working version from
you other installation.)

Let me know how you get on.
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 Sun Feb 06 2005 - 18:53:01 PST
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