I received the files. I reproduced the segfault, and I'm inspecting.
On Wed, Mar 4, 2015 at 4:29 PM, Sanmeet Chahal <schah063.uottawa.ca> wrote:
> Hello all,
>
> I have been trying to send the following message but I don't think it has
> reached you as I do not see it present in the AMBER Mailing list archive,
> please excuse me if this has reached you and you hadn't had the time to
> respond.
>
> I am attaching the prmtop and inpcrd files for all three runs that
> succeeded as well as the the case were it failed (the one for acetic acid).
>
> Legend for the prmtop and inpcrd files attached:
> prmtop, inpcrd correspond to the same molecule show in Tutorial B0.
> prmtop2, inpcrd2 correspond to the molecule shown in Tutorial B0 but the
> methyl group removed from the central carbon.
> prmtop3, inpcrd3 correspond to the molecule shown in Tutorial B0 with atoms
> on half the molecule being removed.
> prmtop4, inpcrd4 correspond to acetic acid (that failed).
>
> I have also attached the input files that I used (they were the same for
> all the runs) and the 01_Min.out and 01_Min.mdinfo files for the run that
> failed.
>
> Also I was using sander from Amber14.
>
> I am sending three emails to keep the size of the attachments below the
> requirements. In this message you will find all the *.in files, the first
> set of prmtop and inpcrd files and the 01_Min.mdout and 01_Min.out files
> for the run that failed.
>
> Thanks,
> Sanmeet
>
> On Wed, Mar 4, 2015 at 8:10 AM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
> > On Tue, Mar 03, 2015, Sanmeet Chahal wrote:
> > >
> > > I am a new Amber user and so I followed and completed Tutorial B0 up to
> > the
> > > point of VMD visualization of the result.
> > >
> > > I am now trying to repeat the tutorial up to this point with a prmtop
> and
> > > inpcrd files that I produce using tleap and a customized frcmod file.
> > Here
> > > are the steps I take:
> >
> > >
> > > I have attached images of the molecules with which I was able to
> complete
> > > the tutorial using prmtop and inpcrd files produced with steps 1-6.
> >
> > We will need to get the actual prmtop and inpcrd files to try to debug
> > a segfault problem. Was there any output in the mdout file from the
> > minimzation step that failed?
> >
> > ...thanks...dac
> >
> >
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> >
>
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 04 2015 - 14:00:07 PST
