Hi, I found the problem :)
addIonsRand replaces random solvent molecules with ions, and to grab a
solvent molecule's position uses its imaging atom. The problem is that for
some reason TIP4P water doesn't have an imaging atom. In solvent.lib the
entries for TIP4PEWBOX and TIP4PBOX have an imaging atom index of 0:
!entry.TIP4PEWBOX.unit.residues table str name int seq int childseq int
startatomx str restype int imagingx
"WAT" 1 5 1 "w" 0
"WAT" 10002 5 5 "w" 0
"WAT" 20003 5 9 "w" 0
... etc
Is this the expected behavior for TIP4 water? I am not sure what the
imaging atom is actually used for as I was just using it to grab the
position of a solvent molecule. From looking at the code I was under the
impression that all water molecules should have an imaging atom.
The TIP3PBOX gives an imaging atom for each water molecule:
!entry.TIP3PBOX.unit.residues table str name int seq int childseq int
startatomx str restype int imagingx
"WAT" 1 4 1 "w" 1
"WAT" 2 4 4 "w" 4
... etc
I can make addIonsRand get the solvent molecules another way if this is the
expected behavior for TIP4P boxes.
Robin
On Mon, Feb 18, 2013 at 2:05 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Apologies for neglecting to attach the PDB:
>
> On Mon, Feb 18, 2013 at 4:54 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > Hello,
> >
> > I'm running tleap on a ribozyme (PDB attached) with the following script:
> >
> > # Constant pH resource file
> > source leaprc.constph
> > # TIP4Pew water model
> > loadAmberParams frcmod.tip4pew
> > loadOFF tip4pewbox.off
> > loadAmberParams frcmod.ionsjc_tip4pew
> >
> > rib = loadPDB 2OUE.pdb
> >
> > solvateOct rib TIP4PEWBOX 20.0
> >
> > addIonsRand rib Na+ 67 Cl- 10
> >
> > saveAmberParm rib 2OUE.solv20.parm7 2OUE.solv20.rst7
> >
> > quit
> >
> > And I get a segfault during the ion adding stage. When I take away the
> > rand, ions are added appropriately.
> >
> > Any ideas?
> >
> > Thanks!
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Tue Feb 19 2013 - 16:00:02 PST
