sounds like you probably didn't compile properly. we don't know anything
about how you did that so can't help.
if you pla to upgrade to Amber 11 when it is released in a few weeks, the
NEB method is completely updated, support larger systems and explicit
solvent, and is much easier to use. it might be worth waiting if you haven't
already started your NEB project.
On Tue, Apr 20, 2010 at 12:11 AM, jani vinod <genomejani.gmail.com> wrote:
> hello ross,
> Thanks for reply
> Sorry, I misinterperated the path intergral dynamics input with NEB and
> used sander.les.mpi
> I generated the Input prmtop and inpcrd files for NEB using addles
> but when I am using sander.MPI the sander get crashed stating
>
> Flags: MPI USE_MPI_IN_PLACE
> *** THIS VERSION WILL NOT ACCEPT TOPOLOGY FILES
> THAT WERE CREATED BY ADDLES, WITH NPARM=1
> USE A VERSION COMPILED WITH -DLES
>
> And when i am trying to compile sander using -DLES option i am gettin g
> following error
>
> undefined reference to `EVB_PIMD_INIT.in.EVB_PIMD'
> runmd.o(.text+0x9dba): In function `runmd_':
> : undefined reference to `EVB_PIMD_DEALLOC.in.EVB_PIMD'
> runmd.o(.text+0x10474): In function `runmd_':
> : undefined reference to `nose_hoover_init_les__'
>
>
> thanks
>
>
>
> On Tue, Apr 20, 2010 at 2:00 AM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
>
> > Hi Jani,
> >
> > > I am trying to run the Nudged Elastic Band Approach tutorial* *with
> > > amber10.
> > > In amber10 manual it is giving that their no separate sander.pimd.MPI
> > > for
> > > amber10 and one has to use sander.LES.MPI
> >
> > Where did you find this in the manual since it is not correct. From Page
> > 134
> > of the AMBER 10 manual:
> >
> > "The NEB capability is implemented inside sander.MPI because of the
> > similarity between
> > PIMD and NEB. Input prmtop and inpcrd files for NEB should be generated
> > using addles"
> >
> > You should use sander.MPI (NO LES).
> >
> > If you let me know where in the manual it refers to sander.LES.MPI I will
> > make sure a correction is posted.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | Assistant Research Professor |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may
> not
> > be read every day, and should not be used for urgent or sensitive issues.
> >
> >
> >
> >
> >
> >
> > _______________________________________________
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> >
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Received on Tue Apr 20 2010 - 03:30:04 PDT
