Re: [AMBER-Developers] addIonsRand command segfaulting

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 18 Feb 2013 17:05:47 -0500

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



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Received on Mon Feb 18 2013 - 14:30:03 PST
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