Re: [apbs-users] [AMBER] iapbs installation

[Jason S. <jas...@gm...>]

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 <ro...@uc...> 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:mig...@af...
> > 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.
> > >
> > (...)
> >
> >
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-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032