Dear all,
with a new "pull" from origin/master, the problem due to sander in the decomposition of mm_pbsa.pl is gone. Thanks to whoever solved this.
Now, we do get rather large differences (multiple kcal/mol) for some of the residues in the PB polar part, however. Can this be related to your changes, Qin:
commit 61a23928d8bc74bcd9f8b67dd15e000b4371bf0a
Author: Qin <qcai.uci.edu>
Date: Thu Mar 1 19:38:59 2012 -0800
Changed default PBSA options in mmpbsa
Updated mmpbsa test cases and nab pbsa test case
Do you mean mm_pbsa.pl with the above "mmpbsa"? Did you update these test cases as well?
Best regards
Holger
On 02.03.12, Scott Brozell wrote:
> Hi,
>
> Thanks Robin.
>
> Here's some more info.
> idecomp1 fails in b05491629eacb62bb34ae8c74cfac2d7bcc6df06
> idecomp1 works in 9dde74cd71e6427297df86e36916277ba567d418
> build fails in bd6332a184ee45af93a644426bd05091817621b5 :
> gfortran -c -O0 -ffree-form -I../../AmberTools/src/pbsa -I../../AmberTools/src/sqm -I../../AmberTools/src/rism -I../../include -I/nfs/10/srb/amber/tmp/amber/include -o sander.o sander.F90
> In file sander.F90:118
> use amd_mod
> 1
> Fatal Error: Can't open module file 'amd_mod.mod' for reading at (1): No such file or directory
>
>
> git log --follow ./src/sander/mdread.F90
> commit b05491629eacb62bb34ae8c74cfac2d7bcc6df06
> Author: Jason Swails <jason.swails.gmail.com>
> Date: Tue Feb 21 17:01:51 2012 -0500
>
> Fix a bug in setting C-terminal radii for mbondi3 radii in ParmEd.
> Thanks to James Maier for catching this!
> Also remove a spurious tab from mdread.F90, it appeared red in my
> syntax highlighting. Red...
>
> commit bd6332a184ee45af93a644426bd05091817621b5
> Author: Romelia <rsalomonferrer.ucsd.edu>
> Date: Tue Feb 14 17:40:06 2012 -0800
>
> RSF added Accelerated Molecular Dynamics to Sander.
> Cleaned AMD routines in pmemd
>
> commit 9dde74cd71e6427297df86e36916277ba567d418
> Author: xiongwu <wuxw.nhlbi.nih.gov>
> Date: Tue Feb 14 13:28:14 2012 -0500
>
> Add SGLD reweighting scripts
> Update SGLD, EMAP reference
> Add option to fix center of mass
>
>
> So now the debuggers have a 3.5 hr time frame to investigate.
>
> scott
>
> ps run the tests, all the tests, for every commit
> and save us all time.
>
>
> On Fri, Mar 02, 2012 at 12:06:48PM -0800, Robin Betz wrote:
> > I went through the logs on the Cruise Control machine and it looks like the
> > failure of idecomp1 predates the start of Cruise Control running tests, as
> > the error is in the very first test log available, on February 14 2012 and
> > has persisted in each build up to now.
> >
> > On Fri, Mar 2, 2012 at 11:36 AM, Scott Brozell <sbrozell.rci.rutgers.edu>wrote:
> > > btw a few targeted monkey darts show that the bug was there 16 days ago:
> > > http://cc.ambermd.org/dashboard/tab/build/detail/Amber_serial_gnu-4.4.5/20120215063112
> > >
> > > On Fri, Mar 02, 2012 at 08:52:37AM -0500, David A Case wrote:
> > > > On Thu, Mar 01, 2012, David A Case wrote:
> > > > > ----- Forwarded message from Holger Gohlke <gohlke.uni-duesseldorf.de>
> > > > > > >
> > > > > > > 1. Many of the "decomposition" tests are failing. Is this
> > > because some
> > > > > > > radii were changed, or because some algorithm was changed? If
> > > there
> > > > > > > is anyone who uses this stuff and can tell what is going on,
> > > that would
> > > > > > > help a lot.
> > > > > >
> > > > > > We saw this as well when we wanted to check in final new .save files
> > > > > > for our examples. The reason must be within sander and was probably
> > > > > > introduced between 13.02.2012 and 28.02.2012. What is troublesome is
> > > > > > that the sum of the internal energies from the decomp. analysis is
> > > not
> > > > > > equal to the sum of these energies from sander.out anymore.
> > > >
> > > > I'd like to see if we can track this down.
> > > >
> > > > 3. Scott: can you poke through the Cruise Control logs to try to
> > > identify the
> > > > spot at which the decomposition tests cases started to fail? That
> > > should help
> > > > us pin down the code change that is causing the problem.
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
--
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Professor fuer Pharmazeutische/Medizinische Chemie
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
Tel.: (+49) 211-81-13662; Fax: (+49) 211-81-13847
Email: gohlke.uni-duesseldorf.de
URL: http://cpclab.uni-duesseldorf.de
++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Sat Mar 03 2012 - 14:30:01 PST
