Can you send me the prmtop files, input file, and a trajectory with ~2 to 3
frames so I can try to reproduce this?
On Thu, Feb 11, 2016 at 7:47 AM, Arati Paudyal <apsilwal123.gmail.com>
wrote:
> Jason,
>
> I tried a short run with AmberTools 15 and I still get the same error
> message. I re-ran the tutorial and it runs fine with AmberTools 15 as well.
>
> On Wed, Feb 10, 2016 at 9:15 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > Have you tried yet with AmberTools 15?
> >
> > On Wed, Feb 10, 2016 at 6:42 PM, Arati Paudyal <apsilwal123.gmail.com>
> > wrote:
> >
> > > Thanks Jason,
> > >
> > > Could you please provide some details on how one might access those
> > hidden
> > > files? Is it stores in some kind of files or do we need to extract it?
> I
> > am
> > > kind of new here in Amber. Any help would be greatly appreciated.
> > >
> > > Also, if I email you the original PDB and prmtop files, is there anyway
> > you
> > > would have time to look at those and see if I am doing anything wrong
> in
> > > separating those two individual PDBs from the complex? I will email
> those
> > > to your gmail if it is ok with you.
> > >
> > >
> > >
> > > Thanks again for your valuable time.
> > >
> > > On Wed, Feb 10, 2016 at 12:00 PM, Jason Swails <jason.swails.gmail.com
> >
> > > wrote:
> > >
> > > > On Wed, Feb 10, 2016 at 10:53 AM, Arati Paudyal <
> apsilwal123.gmail.com
> > >
> > > > wrote:
> > > >
> > > > > Thanks for your reply,
> > > > >
> > > > > I will try to upgrade to Ambertools 15. But since the tutorial
> works
> > > just
> > > > > fine, do you think this could be any issue related to upgrade
> > though? I
> > > > > will follow your suggestion and see how this goes.
> > > > >
> > > >
> > > > We would need to see the output from cpptraj as it tried to compute
> > > > surface areas. There's almost certainly an error message hidden in
> > there
> > > > that will tell us what the problem is.
> > > >
> > > > HTH,
> > > > Jason
> > > >
> > > > --
> > > > Jason M. Swails
> > > > BioMaPS,
> > > > Rutgers University
> > > > Postdoctoral Researcher
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> > > >
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> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 11 2016 - 05:00:07 PST
