Actually, my purpose to compile cpptraj from recent source was to install
latest pytraj, but since pytraj
provides cpptraj functionalities under python environment. So, i tried to
compile it with cpptraj latest version as well.
Now, I will do according to your suggestion and let you know in case of any
problem.
Thank you.
-Shailesh
On Fri, Mar 10, 2017 at 2:38 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> If you need the 'esander' function, your best bet is to stick with
> cpptraj from version AT 16. Otherwise the GitHub version of cpptraj
> with '-nosanderlib' should be fine.
>
> -Dan
>
> On Fri, Mar 10, 2017 at 8:35 AM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in>
> wrote:
> > Thanks you Danial for clarification.
> >
> > So, Now I may try to compile some older snapshot of cpptraj with my
> > AmberTools16. And wait for the release of AmberTools17.
> >
> > On Fri, Mar 10, 2017 at 2:05 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> The sander API has changed since Amber 16 was released, and the GitHub
> >> version of cpptraj has changed with it. So unfortunately you will not
> >> be able to compile GitHub cpptraj with the sander API until the next
> >> release of AmberTools (17), which may occur sometime next month. Until
> >> then you will have to configure GitHub cpptraj with '-nosanderlib'.
> >>
> >> -Dan
> >>
> >> On Fri, Mar 10, 2017 at 5:50 AM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in
> >
> >> wrote:
> >> > Dear All,
> >> >
> >> > I am finding following problem in configuring cpptraj development
> version
> >> > with already compiled ambertools16 which is compiled on the same
> machine
> >> > with same set of tools
> >> >
> >> > Platform:
> >> > Linux Ubuntu 14.04 64 bit
> >> > gcc: gcc (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4
> >> >
> >> > Commands executed.
> >> >
> >> > git clone https://github.com/Amber-MD/cpptraj
> >> >
> >> > cd cpptraj
> >> > echo $AMBERHOME
> >> > /odex/amber16
> >> >
> >> > source $AMBERHOME/amber.sh
> >> >
> >> > bash configure --with-sanderlib=/odex/amber16 -shared -openmp
> -amberlib
> >> gnu
> >> >
> >> > And getting below output. Where is says it Compilation with the SANDER
> >> API
> >> > failed.
> >> > But I want it to compile with sander.
> >> >
> >> > Any suggestion/help in this regard is highly appreciated. If cause of
> >> error
> >> > and solution to it is mentioned it would be a great favor.
> >> >
> >> >
> >> > Assuming 64 bit architecture.
> >> > Enabling position-independent code for generating shared library.
> >> > Using BLAS/LAPACK/ARPACK/NetCDF libraries in /odex/amber16
> >> > Using SANDER API in '/odex/amber16'.
> >> > Using gnu compilers
> >> > Installing cpptraj binary to /home/shailesh/soft/cpptraj/bin
> >> > Using OpenMP
> >> >
> >> > Testing C compiler:
> >> > OK
> >> > Testing C++ compiler:
> >> > OK
> >> > Testing Fortran compiler:
> >> > OK
> >> > Checking BZLIB
> >> > OK
> >> > Checking ZLIB
> >> > OK
> >> > Checking NetCDF
> >> > OK
> >> > Checking LAPACK/BLAS
> >> > OK
> >> > Checking ARPACK
> >> > OK
> >> > Checking availability of the SANDER API from AmberTools
> >> > Using SANDER API from /odex/amber16
> >> > Warning: Compilation with the SANDER API failed. Error follows:
> >> > --------------------
> >> > testp.cpp: In function ‘int main()’:
> >> > testp.cpp:12:44: error: ‘struct sander_input’ has no member named
> >> ‘ibelly’
> >> > input_.ntc = 2; input_.ntr = 0; input_.ibelly = 0;
> >> > ^
> >> > testp.cpp:14:42: error: ‘struct sander_input’ has no member named
> >> > ‘bellymask’
> >> > input_.restraintmask[0] = '\0'; input_.bellymask[0] = '\0';
> >> > input_.refc[0] = '\0';
> >> > ^
> >> > testp.cpp:14:70: error: ‘struct sander_input’ has no member named
> ‘refc’
> >> > input_.restraintmask[0] = '\0'; input_.bellymask[0] = '\0';
> >> > input_.refc[0] = '\0';
> >> >
> ^
> >> > --------------------
> >> >
> >> >
> >> > Thank you,
> >> > Shailesh Panday
> >> > _______________________________________________
> >> > 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Mar 10 2017 - 06:30:03 PST
