Jason,
many thanks. It's been fixed my problem.
James
2014-04-30 15:43 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> On Wed, 2014-04-30 at 14:27 +0400, James Starlight wrote:
> > updated:
> > I've checked bottom of the *.inpcrd and found unfinished file (this time
> > I've not obtained any errors from tleap during saving both topology and
> > coordinates using saveamberparm complex *.prmtop *.inpcrd ) :
> >
> > -19.6220000 -20.4660000 -23.4850000 -23.7830000 -34.9700000 -23.5740000
> > -24.
> >
> >
> > alternatively *.inpcrd file made for the same system using Chimera's GUI
> > looks correct and all md run without problems with it
> >
> > -1.8603000 -40.1806000 -25.3217000 -2.4459000 -23.3482000 -26.1323000
> > -1.6321000 -23.6999000 -25.7724000 -2.6754000 -22.6263000 -25.5479000
> > 64.7160000 75.0900000 72.6290000 90.0000000 90.0000000 90.0000000
> >
> > Finally when I've loaded solvated pdb made by Chimera (including ligand
> > parameters) for checking topology and saving results in new files (using
> > below script) I've obtained brocked *.inpcrd again.
> >
> > source leaprc.ff99SB
> > source leaprc.gaff
> > loadamberparams ligand.frcmod
> > loadoff ligand.lib
> > complex = loadpdb xz.pdb
> > check complex
> > saveamberparm complex 22.prmtop 22.inpcrd
> >
> > How it could be fixed?
>
> I think I found the problem (basically the file handle was never closed
> nor was the content ever flushed -- such behavior is undefined and
> depends on the compiler, kernel, and filesystem to my understanding).
> I've attached a patch that should hopefully fix this problem. I have
> attached a file called leap.patch that is the bug fix that I think will
> work.
>
> To test this, please run the command
>
> cd $AMBERHOME
> ./update_amber --apply path/to/leap.patch
>
> Then you need to recompile leap.
>
> Please let me know if this fixes your problems and I will issue an
> update for it.
>
> Thanks for the report,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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>
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Received on Wed Apr 30 2014 - 07:30:02 PDT
