Hi,
Sorry it took a while for me to get around to fixing this. Should be
fixed in version 7.10.0. See
https://github.com/Amber-MD/cpptraj/pull/1188
I'll have to work on getting a patch into AmberTools.
-Dan
On Wed, Jul 8, 2026 at 3:36 PM Slimak, Stephen Rudolph <SRS215.pitt.edu> wrote:
>
> This work around seems like it's working.
>
> Thanks,
> Stephen
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Wednesday, 08 July 2026 15:11:26
> To: Slimak, Stephen Rudolph <SRS215.pitt.edu>; AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] cpptraj giving seg fault
>
> [You don't often get email from daniel.r.roe@gmail.com. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
>
> Hi,
>
> I was able to reproduce your error and it's a strange one! It
> specifically happens when you trajin certain formats (Amber restart,
> Gromacs TRR) file right before another trajectory file. If you reverse
> the order (trajin the trajectory first before the restart) this
> doesn't happen, nor does it happen with other formats. Again, it's a
> really weird bug!
>
> The temporary workaround would be to convert the restart to something
> like DCD and then read that in, e.g.
>
> parm example.parm7
> # Convert to DCD
> trajin parent.ncrst
> trajout tmp.dcd
> run
> clear trajin
> # Use the DCD
> trajin tmp.dcd
> trajin seg.nc
> trajout seg_stripped.nc cdf start 2
> go
> quit
>
> Hopefully that works for you - let me know if not. In the meantime
> I'll start tracking down this bug.
>
> Thanks for the report.
>
> -Dan
>
> On Wed, Jul 8, 2026 at 2:33 PM Slimak, Stephen Rudolph via AMBER
> <amber.ambermd.org> wrote:
> >
> > Hello Amber Community,
> >
> > I am running into an issue with cpptraj when running the following commands:
> >
> > parm example.parm7
> > trajin parent.ncrst
> > trajin seg.nc
> >
> > <I do other commands here including analysis and stripping away waters, but they aren't necessary to reproduce the error>
> >
> > trajout seg_stripped.nc cdf start 2
> > go
> > quit
> >
> > Every time I try this no matter what the topology and trajectory files are, I get a segmentation fault. I am using the latest version of ambertools. Using only one trajin does not produce the error.
> >
> > Thanks,
> > Stephen
> >
> > --
> > Stephen Slimak
> > Postdoctoral Researcher, Chong Lab
> > Department of Chemistry
> > University of Pittsburgh
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
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Received on Thu Jul 16 2026 - 11:30:02 PDT
