Re: problems on IBM AIX

From: David A. Case <>
Date: Fri 13 Sep 2002 07:42:14 -0700

On Thu, Sep 12, 2002, Giovanni Fossati wrote:
> 1* amber6/sander_classic :
> When I try to run it, with the same script that works on linux, I get this
> error message:
> > 1525-090 The NAMELIST READ statement cannot be completed because an
> > incorrect character was encountered in a NAMELIST group name or item
> > name. The program will recover by discontinuing further processing of
> > the READ statement.

Check the variables in the namelist against the variables listed in the
namelist statement in mdread.f. It is too bad that IBM does not provide
any information about which variable it didn't like, so you will have to
figure what is wrong by hand.

> because it can not read my namelist, but still I am puzzled by the fact
> that sander seems to "die" immediately without running a MD... so how
> can it be opening files?

It died because of the namelist problem listed above.

> > Building on: IBM,7040-681 under AIX
> > cc -c -Drs6000 -DNMLEQ -DCLINK_PLAIN -DMEM_ALLOC -DMASSLIB ptraj.c
> > "ptraj.c", line 4385.37: 1506-045 (S) Undeclared identifier transformCheckOverlap.
> > make: 1254-004 The error code from the last command is 1.

You need to use an ANSI-compliant C compiler. It may be enough to just
define -D__STDC__ in your MACHINE file; but check the IBM link on the Amber
web page to see what is really recommended.

Either Tom Cheatham or I need to submit a patch to fix this.

..good luck...dac

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            |
Received on Fri Sep 13 2002 - 07:42:14 PDT
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