Thank you Hai, It worked.
On Fri, Mar 10, 2017 at 4:26 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> Hi,
>
> You can always install pytraj itself from source code. We have the
> development on github: https://github.com/Amber-MD/pytraj
>
> Install:
> http://amber-md.github.io/pytraj/latest/installation.
> html#from-source-code-easy-way-linux-osx
>
> Let us know if you have any Q.
>
> Hai
>
> On Fri, Mar 10, 2017 at 9:25 AM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in>
> wrote:
>
> > 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
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Mar 10 2017 - 08:00:04 PST
