Thanks robin, addions worked!
On Apr 22, 2013 12:07 AM, "Robin Betz" <rbetz.ucsd.edu> wrote:
> 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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> >
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Received on Sun Apr 21 2013 - 22:00:02 PDT
