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
>>
>
>
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Received on Wed Dec 13 2017 - 15:00:02 PST
