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
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Received on Wed Jan 11 2012 - 14:00:03 PST
