Hi Dan,
Actually, never mind, this ended up working. I did not realize that I
needed to compile this on a separate development node that my HPC admin has
set up which includes all of the necessary header files. The development
version of cpptraj compiled fine after compiling on that node with
configure -amberlib gnu followed by make install.
Joe
------
Joseph Baker, PhD
Assistant Professor
Department of Chemistry
C101 Science Complex
The College of New Jersey
Ewing, NJ 08628
Phone: (609) 771-3173
Web: http://bakerj.pages.tcnj.edu/
On Thu, Dec 14, 2017 at 10:30 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> What compiler and version are you using?
>
> -Dan
>
> On Wed, Dec 13, 2017 at 5:32 PM, Baker, Joseph <bakerj.tcnj.edu> wrote:
> > Hi Dan,
> >
> > It's been a bit since I last posted about this, but I've tried to install
> > the github development version of cpptraj (downloaded just today) to get
> > this functionality now. I was running up against a couple of warnings
> about
> > bzlib.h and about the SANDER API during the configure step, but found a
> > message board post that suggested running configure with the -nobzlib and
> > -nosanderlib options, so my configure command is now
> >
> > ./configure -amberlib -nobzlib -nosanderlib
> >
> > my $AMBERHOME is set so no problem there
> >
> > When I run make install I am getting the following output
> >
> > [bakerj.login001 cpptraj-master]$ make install
> > cd src && make install
> > make[1]: Entering directory `/home/hpc/bakerj/cpptraj/
> cpptraj-master/src'
> > g++ -O3 -Wall -DHASGZ -DBINTRAJ -D_LARGEFILE_SOURCE
> > -D_FILE_OFFSET_BITS=64 -I/opt/tcnjhpc/amber16/include -Ixdrfile -c
> -o
> > ActionFrameCounter.o ActionFrameCounter.cpp
> > g++ -O3 -Wall -DHASGZ -DBINTRAJ -D_LARGEFILE_SOURCE
> > -D_FILE_OFFSET_BITS=64 -I/opt/tcnjhpc/amber16/include -Ixdrfile -c
> -o
> > ActionList.o ActionList.cpp
> > In file included from DataSet.h:6:0,
> > from DataSetList.h:4,
> > from DataIO.h:4,
> > from DataFile.h:3,
> > from DataFileList.h:3,
> > from ActionState.h:3,
> > from Action.h:5,
> > from ActionList.h:3,
> > from ActionList.cpp:2:
> > Dimension.h:64:7: internal compiler error: Illegal instruction
> > if ((*X - *(X-1)) - step > 0.00000000000001) {
> > ^~
> > Please submit a full bug report,
> > with preprocessed source if appropriate.
> > See <http://gcc.gnu.org/bugs.html> for instructions.
> > make[1]: *** [ActionList.o] Error 1
> > make[1]: Leaving directory `/home/hpc/bakerj/cpptraj/cpptraj-master/src'
> > make: *** [install] Error 2
> >
> > Have you seen this issue before when trying to compile this cpptraj
> > version?
> >
> > If there is more info that would be useful, I can try to get this for
> you.
> > Thanks!
> >
> > Kind regards,
> > Joe
> >
> >
> > ------
> > Joseph Baker, PhD
> > Assistant Professor
> > Department of Chemistry
> > C101 Science Complex
> > The College of New Jersey
> > Ewing, NJ 08628
> > Phone: (609) 771-3173
> > Web: http://bakerj.pages.tcnj.edu/
> >
> >
> > On Thu, Mar 30, 2017 at 1:44 PM, Baker, Joseph <bakerj.tcnj.edu> wrote:
> >
> >> Thanks, Dan! I'll give this a try. Appreciate it.
> >>
> >> Joe
> >>
> >>
> >> ------
> >> Joseph Baker, PhD
> >> Assistant Professor
> >> Department of Chemistry
> >> C101 Science Complex
> >> The College of New Jersey
> >> Ewing, NJ 08628
> >> Phone: (609) 771-3173
> >> Web: http://bakerj.pages.tcnj.edu/
> >>
> >>
> >> On Thu, Mar 30, 2017 at 8:20 AM, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >>
> >>> Hi,
> >>>
> >>> In the GitHub version of cpptraj (https://github.com/Amber-MD/cpptraj)
> >>> you can specify part of a molecule as the anchor instead of the entire
> >>> molecule. I've found that this usually fixes imaging issues. Just pick
> >>> a residue in your molecule that you would like at the center of the
> >>> unit cell, e.g.:
> >>>
> >>> autoimage anchor :23
> >>>
> >>> Hope this helps,
> >>>
> >>> -Dan
> >>>
> >>> On Wed, Mar 29, 2017 at 10:10 PM, Baker, Joseph <bakerj.tcnj.edu>
> wrote:
> >>> > Hi all,
> >>> >
> >>> > A student of mine has run a simulation of a protein filament (18
> >>> subunits),
> >>> > and the filament tilts a bit in the water box after several hundred
> >>> > nanoseconds of simulation, at which point a monomer at the end of the
> >>> > filament "appears" on the other face of the periodic box. During the
> >>> > simulation I am using iwrap=1.
> >>> >
> >>> > To remedy this we have tried using autoimage in cpptraj leaving the
> >>> anchor
> >>> > molecule as the default molecule (and have tried a few of the other
> >>> > monomers as the anchor as well), but have not been able to
> successfully
> >>> > reconstruct the filament trajectory without the artificial jumps in
> the
> >>> > coordinates of some monomer(s) (depending on the choice of anchor
> >>> molecule).
> >>> >
> >>> > This doesn't impact calculations internal to an individual monomer
> >>> (RMSD,
> >>> > distances, etc), but impacts calculation of the overall filament
> >>> backbone
> >>> > RMSD for example.
> >>> >
> >>> > Are there any suggestions about how to go about addressing this?
> >>> >
> >>> > Thanks for any help.
> >>> >
> >>> > Joe
> >>> >
> >>> > ------
> >>> > Joseph Baker, PhD
> >>> > Assistant Professor
> >>> > Department of Chemistry
> >>> > C101 Science Complex
> >>> > The College of New Jersey
> >>> > Ewing, NJ 08628
> >>> > Web: http://bakerj.pages.tcnj.edu/
> >>> > _______________________________________________
> >>> > AMBER mailing list
> >>> > AMBER.ambermd.org
> >>> > http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >>>
> >>> --
> >>> -------------------------
> >>> Daniel R. Roe
> >>> Laboratory of Computational Biology
> >>> National Institutes of Health, NHLBI
> >>> 5635 Fishers Ln, Rm T900
> >>> Rockville MD, 20852
> >>> https://www.lobos.nih.gov/lcb
> >>>
> >>> _______________________________________________
> >>> 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
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Dec 16 2017 - 16:00:02 PST
