Dear Bill & Jason,
After recompiling the AMBER the errors went away. Thanks for your precious
suggestions.
On Thu, Jan 12, 2012 at 3:08 AM, Jason Swails <jason.swails.gmail.com>wrote:
> I'll also bring your attention to the fact that there are 2 places that
> look like they may be the correct place to add the F radius. There is a
> logic block for gbsa==1 (LCPO) and gbsa==2 (the other method). If I recall
> correctly, then the only code block where this is a fatal error is for
> gbsa==2. Make sure you are adding the F radius to the proper place, then
> recompiling like Bill suggested.
>
> HTH,
> Jason
>
> On Wed, Jan 11, 2012 at 12:08 PM, Bill Miller III <brmilleriii.gmail.com
> >wrote:
>
> > What exactly did you add to mdread.f? And did you make sure to re-compile
> > after altering the code?
> >
> > You should be adding something similar to the patch posted here (
> > http://archive.ambermd.org/201101/0220.html), but using fluoride and its
> > radius instead of sodium.
> >
> > I hope that helps.
> >
> > -Bill
> >
> > On Wed, Jan 11, 2012 at 11:57 AM, Rajesh Singh <
> rajeshsingh2008.gmail.com
> > >wrote:
> >
> > > Dear All,
> > >
> > > Whenever I'm trying to run MMPBSA-Free Energy Decompostion there are
> > errors
> > > coming. The ligand on which I'm working contains a Fluorine atom
> > > furthermore I tried adding bonding radii of F == 1.47 in mdread.f" file
> > (in
> > > $AMBERHOME/src/sander/mdread.f). But the error persists.
> > >
> > > I also tried changing the 'f' atom types in the prmtop file to 'F'. But
> > > this also made any difference.
> > >
> > > For PERL script
> > > I tried adding > 'F' = 1.47 radius in mm_pbsa_calceneent.pm but this
> is
> > > also not working.
> > >
> > > If any of you guys know how to tackle this problem, then please let me
> > > know.... The error is as follows:
> > >
> > > #####################################################
> > > Running MMPBSA.MPI on 4 processors...
> > > Reading command-line arguments and input files...
> > > Loading and checking parameter files for compatibility...
> > > ptraj found! Using /opt/amber11/bin/ptraj
> > > sander found! Using /opt/amber11/bin/sander for GB calculations
> > > Preparing trajectories for simulation...
> > > [root.localhost MMPBSA]# 500 frames were read in and processed by
> ptraj
> > > for
> > > use in calculation.
> > >
> > >
> > > Beginning GB calculations with sander...
> > > calculating complex contribution...
> > > bad atom type: f
> > > bad atom type: f
> > > bad atom type: f
> > > bad atom type: f
> > > close failed in file object destructor:
> > > IOError: [Errno 9] Bad file descriptor
> > > #####################################################
> > >
> > >
> > >
> > > Thanks & regards
> > > --
> > > Rajesh Singh
> > > NIPER <rajeshsingh2008.gmail.com>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
RAJESH SINGH
PhD Scholar
NIPER
<rajeshsingh2008.gmail.com>
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Received on Thu Jan 12 2012 - 08:30:03 PST
