Dear Amber Users,
I am trying to patch plumed 1.3 with Amer 12 and while executing the this
command : [root.leelab01 amber12]# ./plumedpatch_sander_11.sh -patch
I am getting the following error:
* I will try to patch PLUMED version 1.3 ...
-- Executing pre script
-- Setting up symlinks
-- Applying patches
patching file ./src/sander/Makefile
Hunk #1 FAILED at 119.
Hunk #2 succeeded at 157 with fuzz 2 (offset 9 lines).
Hunk #3 succeeded at 354 (offset -24 lines).
1 out of 3 hunks FAILED -- saving rejects to file ./src/sander/Makefile.rej
patching file ./src/sander/md.h
Hunk #1 FAILED at 19.
Hunk #2 FAILED at 31.
Hunk #3 succeeded at 79 (offset 8 lines).
2 out of 3 hunks FAILED -- saving rejects to file ./src/sander/md.h.rej
patching file ./src/sander/mdread.f
Hunk #1 succeeded at 114 with fuzz 3 (offset -1 lines).
Hunk #2 succeeded at 182 with fuzz 3 (offset -2 lines).
Hunk #3 succeeded at 458 with fuzz 3 (offset -3 lines).
patching file ./src/sander/runmd.f
Hunk #1 succeeded at 563 with fuzz 3 (offset -1 lines).
Hunk #2 succeeded at 684 with fuzz 3 (offset -2 lines).
Hunk #3 succeeded at 1230 with fuzz 3 (offset -3 lines).
patching file ./src/sander/runmin.f
Hunk #1 succeeded at 167 with fuzz 3 (offset -1 lines).
Hunk #2 succeeded at 252 with fuzz 3 (offset -2 lines).
patching file ./src/sander/sander.f
Hunk #1 succeeded at 704 with fuzz 3 (offset -1 lines).
-- Executing post script
- DONE!
=======
There are the contents of Makefile.rej
*** Makefile.preplumed Thu Mar 17 12:20:33 2011
--- Makefile Thu Mar 17 12:24:30 2011
***************
*** 119,125 ****
constantph.o prn_dipoles.o ips.o sglds.o iwrap2.o \
$(AMOEBAOBJ) bintraj.o \
spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o molecule.o
xref.o dssp.o \
! charmm.o
FULLPIMDOBJ = pimd_vars.o pimd_force.o pimd_init.o cmd_vars.o
cmd_matrix.o
--- 119,129 ----
constantph.o prn_dipoles.o ips.o sglds.o iwrap2.o \
$(AMOEBAOBJ) bintraj.o \
spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o molecule.o
xref.o dssp.o \
! charmm.o $(METAOBJ)
!
! include plumed.inc
!
! METAOBJ=$(PLUMED_OBJECTS)
FULLPIMDOBJ = pimd_vars.o pimd_force.o pimd_init.o cmd_vars.o
cmd_matrix.o
=====
There are the contents of md.h.rej
*** md.h.preplumed Thu Mar 17 12:26:51 2011
--- md.h Thu Mar 17 12:29:40 2011
***************
*** 19,25 ****
neb,vv,tmode,ipol,iesp,ievb,nodeid,num_noshake, &!59
idecomp,icnstph,ntcnstph,maxdup,numexchg,repcrd,numwatkeep,hybridgb, &!67
ibgion,ienion,profile_mpi, &!70
! ipb, inp !72
common/mdi/nrp,nspm,ig, & !3
ntx,ntcx,ntxo,ntt,ntp,ntr,init,ntcm,nscm, &
!12
--- 19,26 ----
neb,vv,tmode,ipol,iesp,ievb,nodeid,num_noshake, &!59
idecomp,icnstph,ntcnstph,maxdup,numexchg,repcrd,numwatkeep,hybridgb, &!67
ibgion,ienion,profile_mpi, &!70
! ipb, inp, & !72
! plumed !73
common/mdi/nrp,nspm,ig, & !3
ntx,ntcx,ntxo,ntt,ntp,ntr,init,ntcm,nscm, &
!12
***************
*** 31,39 ****
iwrap,nrespa,irespa,nrespai,icfe,rbornstat, &
!52
ivcap,iconstreff,idecomp,klambda,icnstph,ntcnstph,maxdup,neb,vv,
&!61
tmode,ipol,iesp,ievb,nodeid,num_noshake,ibgion,ienion, &
!69
! profile_mpi,ipb, inp
!72
! parameter (BC_MDI=72) ! Number of elements in the common block;
! Be sure to update if you change things
! ... floats:
--- 32,40 ----
iwrap,nrespa,irespa,nrespai,icfe,rbornstat, &
!52
ivcap,iconstreff,idecomp,klambda,icnstph,ntcnstph,maxdup,neb,vv,
&!61
tmode,ipol,iesp,ievb,nodeid,num_noshake,ibgion,ienion, &
!69
! profile_mpi,ipb, inp ,plumed
!73
! parameter (BC_MDI=73) ! Number of elements in the common block;
! Be sure to update if you change things
! ... floats:
================
Could anybody please tell me how can I patch plumed 1.3 with Amber 12? or
is there any other version of plumed which works with Amber 12?
Thanks in advance for your help.
P.S. I want to use plumed specifically for a Metadynamics Study. I have
posted this question in Plumed forum as well
Regards
BHARAT
--
*Best Regards*
Bharat
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Received on Thu Jul 07 2016 - 18:30:03 PDT
