You can stop sending the files.
On Wed, Mar 4, 2015 at 4:32 PM, Sanmeet Chahal <schah063.uottawa.ca> wrote:
> Here are the prmtop2, inpcrd2, inpcrd3 files.
>
> Sanmeet
>
> 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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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
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>
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 04 2015 - 14:00:09 PST
