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
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> _______________________________________________
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Received on Thu May 30 2019 - 20:30:03 PDT
