Name: amber Version: 11.1.5 Release: 0%{?dist} SOURCE0: amber-11.1.5.tar.bz2 Summary: A suite of programs for molecular dynamics simulations License: GPLv2+ Group: Applications/Scientific BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) BuildRequires: gcc-gfortran BuildRequires: gcc-c++, mpich2, mpich2-devel BuildRequires: libXt, libXt-devel, libXext, libXext-devel BuildRequires: mvapich2, mvapich2-devel BuildRequires: flex perl-Parallel-ForkManager Packager: Hugo R Hernandez %description Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations.[1, 2] The term amber is also sometimes used to refer to the empirical force fields that are implemented here.[3, 4] It should be recognized however, that the code and force field are separate: several other computer packages have implemented the amber force fields, and other force fields can be implemented with the amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools, a collection of freely available programs mostly under the GPL license, and Amber11, which is centered around the sander and pmemd simulation programs. %prep %setup -q %build rm -rf %{buildroot} # Add global env vars export AMBERHOME=$RPM_BUILD_DIR/%{name}-%{version} ; cd ${AMBERHOME}/AmberTools/src ; ./configure gnu %install echo "Install AmberTools v1.5...." mkdir -p %{buildroot}/usr/share export AMBERHOME=$RPM_BUILD_DIR/%{name}-%{version} ; cd ${AMBERHOME}/AmberTools/src ; make install echo "Install Amber for serial jobs...." export MPI_HOME=/usr/lib64/mpich2 export PATH=${PATH}:/usr/lib64/mpich2/bin cd $AMBERHOME ; ./AT15_Amber11.py ; cd src ; make clean && make serial echo "Install parallel binaries...." cd ${AMBERHOME}/AmberTools/src ; make clean ; ./configure -mpi gnu ; make parallel cd ${AMBERHOME} ; ./AT15_Amber11.py ; cd src ; make clean && make parallel mv ${AMBERHOME}/examples %{buildroot}/usr/share/examples mv ${AMBERHOME}/dat %{buildroot}/usr/share/dat mv ${AMBERHOME}/bin %{buildroot}/usr/share/bin mv ${AMBERHOME}/test %{buildroot}/usr/share/test mv ${AMBERHOME}/lib %{buildroot}/usr/share/lib mv ${AMBERHOME}/include %{buildroot}/usr/share/include mv ${AMBERHOME}/share/* %{buildroot}/usr/share/. mv ${AMBERHOME}/doc %{buildroot}/usr/share/doc mv ${AMBERHOME}/AmberTools %{buildroot}/usr/share/AmberTools mv ${AMBERHOME}/benchmarks %{buildroot}/usr/share/benchmarks mkdir %{buildroot}/usr/share/src ; mv ${AMBERHOME}/src/mm_pbsa %{buildroot}/usr/share/src/mm_pbsa %files %defattr(-,root,root) %{_datadir} %{_datadir}/AmberTools %{_datadir}/AmberTools/test %{_datadir}/AmberTools/test/ambpdb %{_datadir}/AmberTools/test/ambpdb_first_protein %{_datadir}/AmberTools/test/ambpdb_first_rna %{_datadir}/AmberTools/test/antechamber %{_datadir}/AmberTools/test/chamber %{_datadir}/AmberTools/test/cpptraj %{_datadir}/AmberTools/test/elsize %{_datadir}/AmberTools/test/leap %{_datadir}/AmberTools/test/mdgx 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