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