Thanks Robert!  I've applied the patch to the development version and will issue a bugfix shortly.

All the best,
Jason

On Sat, Dec 8, 2012 at 8:41 PM, Robert Konecny <rok@ucsd.edu> wrote:
Hi Miguel,

there seems to be a typo in $AMBERHOME/bin/MMPBSA_mods/createinput.py which
leads to a wrong 'srfm' parameter to be used in the calculation. I'm
attaching a small patch to that file which should fix it.

Best,

Robert


On Fri, Dec 07, 2012 at 10:39:12AM +0100, Miguel Ortiz Lombardía wrote:
> Hi Robert,
>
> You are absolutely right concerning compilers. Even if the intel
> compilers are "gcc compatible", they are so with gcc 4.2.1 and not with
> gcc 4.6.2, which I was using. To make sure I do not fall in runtime
> errors due to incompatibilities, I have recompiled the whole thing with
> the intel compilers (icc version 12.1.6 (gcc version 4.2.1 compatibility))
>
> The only changes required are at the configure steps:
>
> CC=icc CXX=icpc FC=ifort F77=ifort ./configure (...)
>
> I can confirm that this also succeeds compiling APBS / iAPBS / sander.APBS.
>
> Thanks!
>
> --
> Miguel Ortiz Lombardía
>
> Architecture et Fonction des Macromolécules Biologiques (UMR7257)
> CNRS, Aix-Marseille Université
> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
> Tel: +33(0) 491 82 55 93
> Fax: +33(0) 491 26 67 20
> mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr
> http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
>
> Le 06/12/12 21:28, Robert Konecny a écrit :
> > Hi Miguel,
> >
> > that's a good news. I'm a bit surprised that your compilation succeeded
> > since it seems like you are using GNU compilers for APBS and iAPBS
> > compilation and then the Intel compilers for Amber. In my experience
> > compiler mixing rarely works.
> >
> (...)
>
> ------------------------------------------------------------------------------
> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
> Remotely access PCs and mobile devices and provide instant support
> Improve your efficiency, and focus on delivering more value-add services
> Discover what IT Professionals Know. Rescue delivers
> http://p.sf.net/sfu/logmein_12329d2d
> _______________________________________________
> apbs-users mailing list
> apbs-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/apbs-users

_______________________________________________
AMBER mailing list
AMBER@ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber




--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032