Re: [AMBER-Developers] cygwin issues

From: Gustavo Seabra <>
Date: Thu, 7 Jan 2010 15:07:22 -0300

On Thu, Dec 31, 2009 at 7:34 PM, Mengjuei Hsieh <> wrote:
> On Thu, Dec 31, 2009 at 09:34:02AM -0500, case wrote:
>> On Wed, Dec 30, 2009, Mengjuei Hsieh wrote:
>> > By the way, sleap test gave me a crash on cygwin, I'll take a look to
>> > see if there is something stupid in my cygwin installation.
>> Do some things work? For me, sleap on cygwin doesn't work at all.  (Type
>> "sleap" and it exits after a few seconds, never even giving a prompt.  See
>> Note 1 at
> Yes, some of the sleap test works and I do have a prompt after I run
> sleap command. I am probably just lucky to be able to run it.
> Nevertheless, there are only two test.sleap crashes in my new cygwin
> install.
> (Attached file is my current cygwin package list just in case.)
> Happy new year.
> --
> Mengjuei Hsieh, Luo Research Group, Molecular Biology & Biochemistry,
> University of California Irvine.

Hi there,

I know it's been a while, but I just wanted to add here that most
AmberTools tests worked just fine with my install of Cygwin 1.7. There
were some failures, though. In sleap, most failures were due to some
escape characters appearing on the messages:

< [gtkleap]$ set default echo on
> ^[[?1034h[gtkleap]$ set default echo on
This same difference appears for the tests:
  o propdiol: test{1,2}.out.dif
  o molinfo:  leap.out.dif
  o prmtop: box.out.dif
  o source: source.out.dif
- In the DNA test, there are differences in the 132d.mol2 file, where
DG was replaced by DG5 and DC by DC3. New standard?
- Sleap does segfault in two cases: amoeba/Run.amoeba_sol and pdbent/Run.pdbent2
All remaining "failures" are roundoff errors that can be ignored. For
completeness, I'm attaching my cygcheck output here, obtained with :
$ cygcheck -s -v -r -h > cygcheck_output.txt
Cheers, and Happy New Year to everyone!
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7450 Ext. 5021
Sent from Recife, Pernambuco, Brazil

AMBER-Developers mailing list

Received on Thu Jan 07 2010 - 10:30:03 PST
Custom Search