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
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Received on Wed Jan 11 2012 - 09:30:02 PST
