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>
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Received on Wed Jan 11 2012 - 09:00:04 PST
