1，超级用户下装intel编译器-ifort
./install.sh
不必细说，有.lic的选2，没有的去邮箱注册选1
2,一般用户下环境变量：
#####MPICH2#####
export MPI_HOME=/home/program/mpich2
export MPICH_HOME=/home/prgram/mpich2
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH: $MPI_HOME/lib
PATH=$PATH: $MPI_HOME/bin
##############amber9########
AMBERHOME=/home/program/amber9
export AMBERHOME
export PATH=$PATH:/home/program/amber9/exe
############IFC##########
source /opt/intel/fce/9.0/bin/ifortvars.sh
export FC=/opt/intel/fce/9.0/bin/ifort----这个根据你安的编译器而定，我安64位用的这个，32位，就用的****/fc/***
### MPI ###
export MPICH_HOME=/home/program/mpich2
export MPI_HOME=/home/program/mpich2
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH: $MPI_HOME/lib
PATH=$PATH: $MPI_HOME/bin
3,一般用户下装amber
A,解压amber9
B, 打补丁 下载 bigfix.all,复制到 amber9的文件夹下
patch -p0 -N -r path-rejects <bugfix.all
C,安装串行版，
cd src
./configure ifort ---选择跟自己系统相匹配的选项 用uname -m 看一下即可知道 eg:./configureifort_x86_64
make serial
cd
cd test
make test
D,安装并行版
mpich2-1.0.1
a, 安装mpich2
./configure -prefix=/home/program/mpich2（--disable-weak-symbols）
make
make install
cd
| touch .mpd.conf|
|chmod 600 .mpd.conf|
|vi .mpd.conf|every user needs done again!
|输入：secretword=ok|
|保存，退出|
|mpd&|
b, 并行安装
cd /src
make clean
./configure -mpich2ifort_x86_64
make parallel
cd ..
cd test
export DO_PARALLEL='mpirun -np 2'
make test.parallel
以上仅为小弟学习安装amber9的粗浅经验，有不当之处，还望指正，多谢

总结的非常好，加油 继续努力。。。

cd cytosine; ./Run.cytosine
i7-108_49476 (mpd_connect 346): connect error: Unknown error 18446744073709551614
i7-108_49476 (mpd_socketpair 323): mpd_socketpair: conn failed
i7-108_49476 (_do_mpdrun 700): _do_mpdrun failed to obtain socketpair
mpdrun: job failed; reason=:failed_to_get_socketpair:
./Run.cytosinerogram error
make[1]: *** [test.sander.BASIC] Error 1
make[1]: Leaving directory `/home/program/amber9/test'
make: *** [test.sander.BASIC.MPI] Error 2