Re: [AMBER] autoimage for a protein filament

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 14 Dec 2017 10:30:50 -0500

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
>>>
>>
>>
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-- 
-------------------------
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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Received on Thu Dec 14 2017 - 08:00:03 PST
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