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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Received on Wed Apr 30 2014 - 05:00:02 PDT
