Research:compile amber

sander of amber pre 9 or DARDEN-AMOBEA version

The original source is in /home/pren/DARDEN_amber An example compiled on pluto: /home/pren/AMOEBA/amber-range-soft

 source ~/.cshrc.f10
 cd sander
 make sander

Modified (by socar) source in /home/oscar/data2-oscar/amber_mod_org/

See here for detailed modification http://biomol.bme.utexas.edu/wiki/index.php/Research:Amber_modification

README file in the directory explain the process. Esstially cd SRC/sander and make sander. Other exe won't compile but not needed.

Use intel compiler ver 9! and REDHL or centos 4 (bme-sugar).

Doesn't work on centos 5. error:Invalid GNU version

Intel v 10 will compile but segfault when running on fc 7 or 8.    (were able to compile amber-rang-soft on pluto using intel v10, fc8.; and run OK)

Intel	Platform	Compile	Simulation	Energy minimization
v10	fc8(venus),fc7(neptune),centos5(nova),ranger	YES	YES	NO (prints 1st step, SEG error)
v9	fc7,fc8,fc10,centos5	NO(Invalid GNU version)	N/A	N/A
v9	centos4(sugar)	YES	YES	YES

Tom's orginal instruction in ~pren/DARDEN_amber/README copy the g95_config.h into the unpacked SRC diectory as config.h should be able to go into sander and just say make sander all the amoeba specific stuff in sander directory is named amoeba_adjust.f etc. i.e. amoeba_ prefix the worst of the connection to regular sander is in the list builder and the fft code which are both fast but impenetrable code i include my intel_config.h also---sometimes this is a problem depending on your c compiler and your loader for intel compiler you could try one of the options in configure script in src. remember to set AMBERBUILDFLAGS=-DAMOEBA in the resulting config.h to turn on the amoeba code use icc in intel_config.h extract mdcrd to pdb: /opt/amber7/exe/ptraj pepc.prmtop pepc.scrpt pepc.scrpt: trajin mdcrd trajout tra.pdb pdb

pmemd/amber9 from bob duke

orginal source in /home/pren/pmemd-oscar

Follow COMPILE.readme!

Definitely should work (priot to summer 2008) using intel v9 and RHEL/centos 4.

But you have to remove "–luuid" in config.h

Seems to also work with intel v10 and FC7 or 8.

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bme-sun (fc7) /home/pren/pmdmd-sun

run ./configure linux_em64t ifort mpich2 pubfft < in

remove uuid and add DAMOEBA in config.h (append "-DAMOEBA" to config.h line DEFINE_F90: "F90_DEFINES = -DFFTLOADBAL_2PROC -DAMOEBA")

intel v10
/opt/intel/mkl/8.1
/opt/mpich2

Compilation using /opt/mpichi2 (1.03) works but may need mpich2-fc7 (1.05) to run the actual mpdboot.

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sander in amber 9

The softcor and ion and mdin (taking parameters for ligands and lambda?) modification yet to be transferred to sander/amber9.