plumed 2.3.3 patch to amber14

[jklmko]

Hi, all

I installed plumed 2.3.3 and want to link it to amber14. But when I use “plumed patch -r”, errors occurred. What should I do?

 

PLUMED patching tool

 

1) amber14          4) gromacs-5.0.7    7) namd-2.8

2) gromacs-2016.3   5) gromacs-5.1.4    8) namd-2.9

3) gromacs-4.5.7    6) lammps-6Apr13    9) qespresso-5.0.2

Choose the best matching code/version:1

MD engine: amber14

PLUMED location: /export/apps/plumed-2.3.3/lib/plumed

diff file: /export/apps/plumed-2.3.3/lib/plumed/patches/amber14.diff

sourcing config file: /export/apps/plumed-2.3.3/lib/plumed/patches/amber14.config

Linking Plumed.h and Plumed.inc (shared mode)

Patching with on-the-fly diff from stored originals

ERROR: File ./AmberTools/src/sander/constants.F90 is missing

patching file ./AmberTools/src/sander/Makefile

Hunk #1 succeeded at 18 with fuzz 4.

Hunk #2 succeeded at 377 with fuzz 5 (offset 136 lines).

Hunk #3 FAILED at 254.

Hunk #4 FAILED at 280.

Hunk #5 FAILED at 293.

3 out of 5 hunks FAILED -- saving rejects to file ./AmberTools/src/sander/Makefile.rej

patching file ./AmberTools/src/sander/mdread.F90

Hunk #1 FAILED at 9.

Hunk #2 FAILED at 135.

Hunk #3 succeeded at 254 with fuzz 5 (offset -1 lines).

Hunk #4 succeeded at 591 with fuzz 5 (offset -2 lines).

2 out of 4 hunks FAILED -- saving rejects to file ./AmberTools/src/sander/mdread.F90.rej

patching file ./AmberTools/src/sander/runmd.F90

Hunk #1 succeeded at 47 with fuzz 4.

Hunk #2 succeeded at 361 with fuzz 4 (offset 38 lines).

Hunk #3 succeeded at 797 with fuzz 4 (offset 59 lines).

Hunk #4 succeeded at 1114 with fuzz 4 (offset 160 lines).

Hunk #5 succeeded at 1883 with fuzz 4 (offset 223 lines).

Hunk #6 succeeded at 4303 with fuzz 4 (offset 136 lines).

Hunk #7 succeeded at 4516 with fuzz 4 (offset 136 lines).

patching file ./AmberTools/src/sander/sander.F90

Hunk #1 succeeded at 17 with fuzz 4.

Hunk #2 succeeded at 994 with fuzz 4 (offset 40 lines).

 

PLUMED is compiled with MPI support so you can configure amber14 with MPI

 

I sincerely hope someone can help me!

Thanks.

 

George

[satya...@gmail.com]

 I think you can with this option:
            plumed patch -p
     for patching with your desired MD engine.

 You have used -r  instead of -p  , I think this is the origin of error.

  You can look at this:
    Patching Your MD Code at this site :

    https://plumed.github.io/doc-v2.4/user-doc/html/_installation.html

  Look whether it will work or not......

   Thanks.........

[yesterd...@gmail.com]

if your version of AmberTools is larger than 15, you do not need to patch the code because the official version of latest AmberTools have already include the interface of PLUMED. The only thing you need to do is just to modified the file config.h after running configure. In the end of the file config.h, it should be like this:

# PLUMED related variables:
PLUMED_INCLUDE_FILE=
PLUMED_LOAD=Plumed.o -ldl -Wl,-export-dynamic
PLUMED_DEPENDENCIES=Plumed.o

Added your patch of Plumed.inc file to PLUMED_INCLUDE_FILE like:

# PLUMED related variables:
PLUMED_INCLUDE_FILE=(your_plumed_path)/lib/plumed/src/lib/Plumed.inc
PLUMED_LOAD=Plumed.o -ldl -Wl,-export-dynamic
PLUMED_DEPENDENCIES=Plumed.o

Then to recompile Amber14. Anything will be OK!

Isaac

在 2017年11月29日星期三 UTC+1上午9:55:08，jklmko写道：