Hi,
On Thu, May 30, 2019 at 11:55 PM Reber, David <David.Reber.empa.ch> wrote:
> helpme_standalone.h(991): internal error: assertion failed: node_has_side_effects: bad node kind (shared/cfe/edgcpfe/il.c, line 20802)
OK, it seems like whatever compilers you are using (what version are
they?) have trouble with C++11 constructs. You can disable C++11
support by running configure with the '-noc++11' keyword. This will
disable particle mesh Ewald for the 'energy' command, but if you don't
need that then that's ok.
>
> Then I ran "make check" and encountered several possible failures "file *** does not exist" and I noticed in the .out files in the test folder it still says CPPTRAJ V17.00
If compilation fails, then you won't actually have a cpptraj binary to
test. Make sure that you are sourcing cpptraj.sh or cpptraj.csh in
your cpptraj directory (the directory with 'configure' in it).
Hope this helps,
-Dan
PS - You don't need to copy the amber directory locally - in fact you
probably want to avoid this since there will be some paths that will
be made incorrect by this. The only thing cpptraj needs to configure
with '-amberlib' is to have AMBERHOME pointing to your actual Amber
installation (it only needs to read things from there).
> Also the /AmberTools/src/cpptrajnew/bin/ folder is empty...
>
> Any ideas what went wrong?
>
> Thank for your help!
>
>
>
> > -----Original Message-----
> > From: Thomas Cheatham [mailto:tec3.utah.edu]
> > Sent: Freitag, 31. Mai 2019 05:07
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Radgyr or distance averages
> >
> > I am not an expert, but the error log looks like compiled with Intel compilers,
> > so try configure with the intel instead of gnu. (The AMBERHOME lapack etc
> > are likely not from Gnu).
> > ________________________________________
> > From: Reber, David <David.Reber.empa.ch>
> > Sent: Thursday, May 30, 2019 9:03:49 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Radgyr or distance averages
> >
> > Thank you for that info. I put the new cpptraj in
> > /amber16/AmberTools/src/cpptrajnew and ran ./configure -amberlib gnu
> >
> > I get a test compile error:
> > Testing C++ compiler: OK
> > Testing C compiler: OK
> > Testing Fortran compiler: OK
> > Testing C++11 support: Not present
> > Using blas from /home/guest/amber16
> > Using lapack from /home/guest/amber16
> > Using netcdf from /home/guest/amber16
> > Checking BZLIB: OK
> > Checking ZLIB: OK
> > Checking NetCDF: OK
> > Checking LAPACK/BLAS:
> > Test compile failed: g++ -Wall -O3 -o testp testp.cpp
> > /home/guest/amber16/lib64/liblapack.a
> > /home/guest/amber16/lib64/libblas.a -lgfortran -lpthread
> > Error follows:
> > See attached file
> >
> > Where did I go wrong?
> >
> > > -----Original Message-----
> > > From: Thomas Cheatham [mailto:tec3.utah.edu]
> > > Sent: Freitag, 31. Mai 2019 04:43
> > > To: AMBER Mailing List
> > > Subject: Re: [AMBER] Radgyr or distance averages
> > >
> > >
> > > You can have multiple versions of different programs installed. What one
> > you
> > > run depends on your $path setting or you can use an explicit path
> > > (/user/john/CPPTRAJ/cpptraj/bin/cpptraj) for your specific path. If this is
> > > confusing, learn more about basic UNIX and shells.
> > >
> > > The stand-alone CPPTRAJ should compile on its own and you should not
> > > overwrite the AMBER one (since they are different versions).
> > >
> > > In the *new* cpptraj directory,
> > >
> > > ./configure --help
> > >
> > > for options to compile.
> > >
> > > Give the list feedback for issues, and I will try to work with Dan to make it
> > > simpler and to distinguish the AmberTools version from the Git version... --
> > > tom
> > >
> > >
> > >
> > >
> > > ________________________________________
> > > From: Reber, David <David.Reber.empa.ch>
> > > Sent: Thursday, May 30, 2019 8:33:47 PM
> > > To: AMBER Mailing List
> > > Subject: Re: [AMBER] Radgyr or distance averages
> > >
> > > So do I just delete the existing cpptraj folder, copy the new one into
> > > Ambertools/src/ and run make install?
> > >
> > > > -----Original Message-----
> > > > From: Thomas Cheatham [mailto:tec3.utah.edu]
> > > > Sent: Freitag, 31. Mai 2019 04:23
> > > > To: AMBER Mailing List
> > > > Subject: Re: [AMBER] Radgyr or distance averages
> > > >
> > > > You want the stand-alone CPPTRAJ, see:
> > > >
> > > > https://github.com/Amber-
> > > > MD/cpptraj/blob/master/doc/CpptrajDevelopmentGuide.pdf
> > > > ________________________________________
> > > > From: Reber, David <David.Reber.empa.ch>
> > > > Sent: Thursday, May 30, 2019 8:17:53 PM
> > > > To: AMBER Mailing List
> > > > Subject: Re: [AMBER] Radgyr or distance averages
> > > >
> > > > I have copied the amber16 folder into "my" directory where I have write
> > > > permission, changed $amberhome accordingly and dowloanded the git-
> > > > cpptraj .zip file.
> > > > Could you be so kind to run me through the installation of the new
> > > CPPTRAJ?
> > > >
> > > >
> > > >
> > > >
> > > > > -----Original Message-----
> > > > > From: Thomas Cheatham [mailto:tec3.utah.edu]
> > > > > Sent: Freitag, 31. Mai 2019 04:07
> > > > > To: AMBER Mailing List
> > > > > Subject: Re: [AMBER] Radgyr or distance averages
> > > > >
> > > > >
> > > > > You probably cannot install in the system branch that your "host"
> > > > maintains,
> > > > > but why not just download CPPTRAJ from the Git page and install in
> > your
> > > > > home directory? It is not that big and fairly easy to do....
> > > > > ________________________________________
> > > > > From: Daniel Roe <daniel.r.roe.gmail.com>
> > > > > Sent: Thursday, May 30, 2019 7:39:12 PM
> > > > > To: AMBER Mailing List
> > > > > Subject: Re: [AMBER] Radgyr or distance averages
> > > > >
> > > > > Unfortunately no. The 'for' syntax is pretty recent - I think you'll
> > > > > need at least the AmberTools 18 version.
> > > > >
> > > > > If you have access to compilers, you could try compiling yourself. If
> > > > > the rest of amber is available (and you have access to compilers) it's
> > > > > fairly simple: with AMBERHOME set just './configure -amberlib gnu'
> > > > > followed by 'make install' to build the latest cpptraj.
> > > > >
> > > > > -Dan
> > > > >
> > > > > On Thu, May 30, 2019 at 9:33 PM Reber, David
> > <David.Reber.empa.ch>
> > > > > wrote:
> > > > > >
> > > > > > Hi Dan
> > > > > >
> > > > > > Is there a way around updating? I'm just on an exchange where I'm
> > > > > working at the moment and don't have the rights to update anything.
> > > > > >
> > > > > > David
> > > > > >
> > > > > >
> > > > > > > -----Original Message-----
> > > > > > > From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> > > > > > > Sent: Freitag, 31. Mai 2019 03:29
> > > > > > > To: AMBER Mailing List
> > > > > > > Subject: Re: [AMBER] Radgyr or distance averages
> > > > > > >
> > > > > > > Please upgrade to the github version or the version from
> > ambertools
> > > > 19.
> > > > > > >
> > > > > > > -Dan
> > > > > > >
> > > > > > > On Thu, May 30, 2019 at 9:23 PM Reber, David
> > > > <David.Reber.empa.ch>
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi Dan
> > > > > > > >
> > > > > > > > With "inmask" in one word I get the same error. I'm using Version
> > > > > V17.00.
> > > > > > > >
> > > > > > > > Reading 'MD333.mdcrd' as Amber Trajectory
> > > > > > > > [for residues R0 inmask :FSI i=1;i++]
> > > > > > > > Error: Unrecognized character in expression: :
> > > > > > > > 'for residues R0 inmask :FSI i=1;i++': Invalid command or
> > expression.
> > > > > > > > 1 errors encountered reading input.
> > > > > > > >
> > > > > > > >
> > > > > > > > In the Amber16 manual I cannot find the "inmask" keyword....
> > > > > > > >
> > > > > > > > David
> > > > > > > >
> > > > > > > >
> > > > > > > > > -----Original Message-----
> > > > > > > > > From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> > > > > > > > > Sent: Freitag, 31. Mai 2019 03:15
> > > > > > > > > To: AMBER Mailing List
> > > > > > > > > Subject: Re: [AMBER] Radgyr or distance averages
> > > > > > > > >
> > > > > > > > > Hi,
> > > > > > > > >
> > > > > > > > > The keyword is 'inmask' (all one word - see the manual or type
> > > 'help
> > > > > for'
> > > > > > > > > for syntax). Also, what version of cpptraj are you using?
> > > > > > > > >
> > > > > > > > > -Dan
> > > > > > > > >
> > > > > > > > > On Thu, May 30, 2019 at 8:32 PM Reber, David
> > > > > <David.Reber.empa.ch>
> > > > > > > > > wrote:
> > > > > > > > >
> > > > > > > > > > Hi Dan
> > > > > > > > > >
> > > > > > > > > > I see, thank you for clarification. I tried your suggestion and I
> > get
> > > > > > > > some
> > > > > > > > > > invalid command error messages:
> > > > > > > > > >
> > > > > > > > > > [trajin MD333.mdcrd]
> > > > > > > > > > Reading 'MD333.mdcrd' as Amber Trajectory
> > > > > > > > > > [for residues R0 in mask :FSI i=1;i++]
> > > > > > > > > > Error: Unrecognized character in expression: :
> > > > > > > > > > 'for residues R0 in mask :FSI i=1;i++': Invalid command or
> > > > > expression.
> > > > > > > > > > 1 errors encountered reading input.
> > > > > > > > > >
> > > > > > > > > > Do you see where the problem lies?
> > > > > > > > > >
> > > > > > > > > > Thanks for your help,
> > > > > > > > > > David
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > > -----Original Message-----
> > > > > > > > > > > From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> > > > > > > > > > > Sent: Donnerstag, 30. Mai 2019 17:03
> > > > > > > > > > > To: AMBER Mailing List
> > > > > > > > > > > Subject: Re: [AMBER] Radgyr or distance averages
> > > > > > > > > > >
> > > > > > > > > > > Hi,
> > > > > > > > > > >
> > > > > > > > > > > On Wed, May 29, 2019 at 11:24 PM Reber, David
> > > > > > > > > <David.Reber.empa.ch>
> > > > > > > > > > > wrote:
> > > > > > > > > > > > If I calculate the radius of gyration or atom-atom distances
> > > for
> > > > > > > > one
> > > > > > > > > > > particular molecule in my trajectory I obtain values I would
> > > > expect.
> > > > > > > > > > > > e.g. my 9-atom anion called FSI(resid 1) "radgyr :1 out
> > > ***.dat
> > > > > > > > mass
> > > > > > > > > > > tensor" yields something like 1.9 Angstrom.
> > > > > > > > > > > > If I select all the molecules of a certain type I get values
> > that
> > > > > > > > are
> > > > > > > > > > > approximately half the box size:
> > > > > > > > > > > > "radgyr :FSI out ***.dat mass tensor" yields ca. 20
> > Angstrom.
> > > > > > > > > > >
> > > > > > > > > > > So as you are seeing, by default the atom masks in these
> > > > > commands
> > > > > > > > > > > apply to all atoms. That is, something like :WAT for 'radgyr'
> > will
> > > > > > > > > > > calculate the radius of gyration of *all* water molecules in
> > > your
> > > > > > > > > > > system. So what you would need to do is create a loop over
> > > > > whatever
> > > > > > > > > > > molecules/residues, then calculate the average. So
> > something
> > > > like
> > > > > > > > this
> > > > > > > > > > > should work:
> > > > > > > > > > >
> > > > > > > > > > > parm myparm.parm7
> > > > > > > > > > > trajin mytraj.nc
> > > > > > > > > > > for residues R0 inmask :FSI i=1;i++
> > > > > > > > > > > radgyr rg$i $R0
> > > > > > > > > > > done
> > > > > > > > > > > avg oversets rg* name AvgRg out AvgRg.dat
> > > > > > > > > > > run
> > > > > > > > > > >
> > > > > > > > > > > If you want the individual radius of gyration values for each
> > > > > > > > residue,
> > > > > > > > > > > just add 'out rg.dat' or something to the 'radgyr' command.
> > > > Hope
> > > > > this
> > > > > > > > > > > helps,
> > > > > > > > > > >
> > > > > > > > > > > -Dan
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > > I have the same issue with the distance command. If I
> > select
> > > > two
> > > > > > > > atoms
> > > > > > > > > > on
> > > > > > > > > > > resid 1 I get reasonable values in the range of 3-4 Angstrom:
> > > > > > > > > > > > "distance :1.F1 :1.F2 out distance.dat"
> > > > > > > > > > > >
> > > > > > > > > > > > if I select all FSI-residues, I get values of about 0.2 A:
> > > > > > > > > > > > "distance :FSI.F1 :FSI.F2 out distance.dat"
> > > > > > > > > > > >
> > > > > > > > > > > > In case of the distance command I assume intermolecular
> > > > > distances
> > > > > > > > are
> > > > > > > > > > also
> > > > > > > > > > > calculated which in the end cancel each other out resulting in
> > > the
> > > > > > > > value
> > > > > > > > > > close
> > > > > > > > > > > to zero?
> > > > > > > > > > > >
> > > > > > > > > > > > How can I get the average radgyr or intramolecular atom-
> > > atom
> > > > > > > > > distances
> > > > > > > > > > > for a certain type of molecule averaged over the whole
> > > > > trajectory?
> > > > > > > > > > > >
> > > > > > > > > > > > Thank you in advance for any hints,
> > > > > > > > > > > >
> > > > > > > > > > > > David
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > _______________________________________________
> > > > > > > > > > > > AMBER mailing list
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> > > > > > > > > > >
> > > > > > > > > > >
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Received on Fri May 31 2019 - 07:30:03 PDT
