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
> _______________________________________________
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> 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
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Received on Fri Mar 10 2017 - 05:30:03 PST
