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
>
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Received on Fri Mar 10 2017 - 06:00:04 PST
