Hi Dan,
Thank you for your response. I'm just waiting on the bugfixes that were
used, and then I'll be able to send you a reply to your questions.
Thanks again, and have a great day,
Kamali Sripathi
On Wed, Mar 23, 2011 at 9:45 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> In order to help diagnose the problem we need to try and reproduce it.
> To that end please provide:
>
> 1) Version of ptraj used (e.g. AmberTools 1.4) and bugfixes applied (if
> any)
> 2) Which compilers were used to build ptraj and what version
> 3) The exact ptraj input that causes the error
> 4) The output that ptraj produces
> 5) If possible, attach the topology and restart (or 1 frame of
> trajectory) files of the system you are using. If this is not possible
> for whatever reason, please provide system details, i.e. number of
> atoms, number of frames in traj, whether the system is periodic etc.
>
> Providing all of the above information will make it easier for us to
> understand any bugs that may be occurring and ultimately easier to
> help you.
>
> Thanks!
>
> -Dan
>
> On Wed, Mar 23, 2011 at 9:01 AM, Kamali Sripathi <ksripath.umich.edu>
> wrote:
> > Dear Dr. Cheatham,
> >
> > Thank you very much for your response.
> >
> > On Tue, Mar 22, 2011 at 7:33 PM, Thomas Cheatham III <tec3.utah.edu>
> wrote:
> >
> >>
> >> There is insufficient information provided to comment.
> >>
> >>
> > This is very true; sorry for not being more specific. The ptraj script
> that
> > I'm referring to has about 18 distance commands, one angle command, and
> > three dihedral commands. My system is an RNA system of 85 nucleotides,
> and
> > I've been running simulations on the wild-type structure as well as 8
> > structures with 1 base pair mutated. I slightly modify some distance
> > commands in my ptraj script to apply it to each of the 9 structures. I'm
> > frustrated because it works for, say, mutants 2-8, but I consistently get
> > seg faults when I use it for the wild-type and mutant 1 structures.
> >
> > Please let me know if you need more information.
> >
> > Thanks again, and have a great day,
> >
> > Kamali
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Wed Mar 23 2011 - 12:00:03 PDT
