AMBER Archive (2007)

Subject: Re: AMBER: Error in protonating

From: David A. Case (case_at_scripps.edu)
Date: Sat Apr 28 2007 - 16:26:08 CDT

On Fri, Apr 27, 2007, Neelanjana Sengupta wrote:
>
> In protonating a peptide (coordinates available in pdb format), I use the
> foll. command:
>
> protonate -d PROTON_INFO < peptide.pdb > peptide2.pdb
>
> and, I get the foll. error:
>
> :-) G R O M A C S (-:
> Segmentation fault

This is just a guess: type "which protonate" to be sure that you are running
Amber's version of protonate. The message above looks like it may be coming
from Gromacs.

...good luck...dac

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