Jason,
many thanks for suggestions. The problems was exactly in the root
permissions. By the way from the amber manual I've noticed that in new
realize 3 different way's of MMPBSA calculations are realized. In this
regard I wounder to know 1) if the existing MMPBSA on-line tutorial is
still valid and 2) what exactly MMPBSA method could be better for my task
(analysis of the namd produced dcd trajectories with the conversion of the
psf topologies to amber format)?
Thanks for help,
James
2014-04-21 15:47 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> On Mon, 2014-04-21 at 14:37 +0400, James Starlight wrote:
> > also I've forced with the below error during compilation of the amber
> > without cuda using gcc 4.7 (all the required packages listed in manual
> have
> > been installed|)
> >
> > r14/lib/libemil.a -lstdc++ \
> > ../sebomd/sebomd.a \
> > ../lib/sys.a
> > /home/own/Documents/simulations/amber/amber14/lib/libnetcdff.a
> > /home/own/Documents/simulations/amber/amber14/lib/libnetcdf.a \
> > -lrism -lfftw3 -larpack -llapack -lblas \
> >
> > /usr/bin/ld: cannot find -lstdc++
> > collect2: error: ld returned 1 exit status
> >
> > How does it possible to install amber tools (in particular i need only
> for
> > the lattest mmpbsa) in minimal set ?
>
> We don't have enough information about your system to help here.
> libstdc++ is a (very) common library that should be on (almost) every
> system. My suspicion is that you do not have a C++ compiler installed.
> Make sure you have installed all of the prerequisites for Amber first:
>
> http://ambermd.org/ubuntu.html
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
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Received on Mon Apr 21 2014 - 08:00:03 PDT
