Hi Jonathan,
This is a bug with addIonsRand and TIP4 water that is fixed in the upcoming
release of AmberTools13.
If you use addIons instead the segmentation fault will not occur.
Hope this helps,
Robin Betz
On Sun, Apr 21, 2013 at 8:09 PM, Jonathan Gough
<jonathan.d.gough.gmail.com>wrote:
> Dear Gurus,
>
> Not sure why this is happening. I tried it a few times.
>
> Using Amber12, AmbverTools12, tleap, MacOSX
>
> here is a summary:
>
> loaded external parameters frcmod, off, (phosphothreonine and
> phosphoserine)
> loaded pdb
> saved pdb
> saved prmtop inpcrd
> loaded TIP4Pew parameters
> solvated in a TIP4PewBOX 12.0
> addionsrand Na+ 0
>
> then leap just crashes
>
> (using default radius 1.500000 for EPW)
> Total vdw box size: 110.230 154.077 120.389 angstroms.
> Volume: 2044656.144 A^3
> Total mass 1073041.258 amu, Density 0.871 g/cc
> Added 51554 residues.
> > addionsrand com Na+ 0
> 15 Na+ ions required to neutralize.
> Adding 15 counter ions to "com". 51539 solvent molecules will remain.
> /Users/jonathangough/amber12/bin/tleap: line 17: 61658 Segmentation fault:
> 11 $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep
> -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm
> -I$AMBERHOME/dat/leap/cmd $*
>
> any thoughts?
>
> Thanks,
> JOnathan
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Received on Sun Apr 21 2013 - 21:30:02 PDT
