Dear Amber Users,
I have been running some tests with the MM-PBSA suite of perl scripts. I
have come across a similar errors as other users faced while doing so.
Error i have gone through is:
Reading snapshot_com.all.out
WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
WARNING: Missing PB for PB in 0 -> Taken from -1
WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
WARNING: Missing PBCAV for PB in 0 -> Taken from -1
WARNING: Missing EPB for PB in 0 -> Taken from -1
WARNING: Missing PBDIS for PB in 0 -> Taken from -1
WARNING: Missing SURF for MS in 0 -> Taken from -1
WARNING: Missing PBNONPOL for PB in 1 -> Taken from 0
WARNING: Missing ELRAELE for PB in 1 -> Taken from 0
WARNING: Missing EPB for PB in 1 -> Taken from 0
WARNING: Missing PBNONPOL for PB in 2 -> Taken from 1
WARNING: Missing ELRAELE for PB in 2 -> Taken from 1
WARNING: Missing EPB for PB in 2 -> Taken from 1
WARNING: Missing PBNONPOL for PB in 3 -> Taken from 2
WARNING: Missing ELRAELE for PB in 3 -> Taken from 2
WARNING: Missing EPB for PB in 3 -> Taken from 2
WARNING: Missing PBNONPOL for PB in 4 -> Taken from 3
WARNING: Missing ELRAELE for PB in 4 -> Taken from 3
WARNING: Missing EPB for PB in 4 -> Taken from 3
WARNING: Missing PBNONPOL for PB in 5 -> Taken from 4
WARNING: Missing ELRAELE for PB in 5 -> Taken from 4
When i Google regarding the error, I found a way to fix the problem from
previous mailing list.
As per the suggestions from previous mails,
I tried to patch the latest bug fixes for Amber10. But i faced problem
while patching as follows
*
Hunk #3 FAILED at 660.
Hunk #4 FAILED at 1146.
Hunk #5 FAILED at 1158.
Hunk #6 FAILED at 1178.
6 out of 6 hunks FAILED -- saving rejects to file src/sander/runmd.f.rej
patching file src/sander/sander.f
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file src/sander/sander.f.rej
patching file src/etc/elsize.cc
Hunk #1 FAILED at 71.
1 out of 1 hunk FAILED -- saving rejects to file src/etc/elsize.cc.rej
patching file src/sander/qm2_load_params_and_allocate.f
Reversed (or previously applied) patch detected! Skipping patch.
15 out of 15 hunks ignored -- saving rejects to file
src/sander/qm2_load_params_and_allocate.f.rej
patching file src/sander/qm2_scf.f
Reversed (or previously applied) patch detected! Skipping patch.
5 out of 5 hunks ignored -- saving rejects to file src/sander/qm2_scf.f.rej
patching file src/sander/dynlib.f
Hunk #1 FAILED at 164.
Hunk #2 FAILED at 205.
2 out of 2 hunks FAILED -- saving rejects to file src/sander/dynlib.f.rej
patching file src/sander/files.h
Hunk #1 FAILED at 5.
Hunk #2 FAILED at 23.
2 out of 2 hunks FAILED -- saving rejects to file src/sander/files.h.rej
patching file src/sander/mdfil.f
Reversed (or previously applied) patch detected! Skipping patch.
4 out of 4 hunks ignored -- saving rejects to file src/sander/mdfil.f.rej
patching file src/sander/mdread.f
Hunk #1 FAILED at 127.
Hunk #2 succeeded at 1745 with fuzz 2 (offset 16 lines).
1 out of 2 hunks FAILED -- saving rejects to file src/sander/mdread.f.rej
patching file src/sander/trajene.f
Reversed (or previously applied) patch detected! Skipping patch.
5 out of 5 hunks ignored -- saving rejects to file src/sander/trajene.f.rej
The next patch would create the file test/trajene/mdcrd.out.save,
which already exists! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
test/trajene/mdcrd.out.save.rej
patching file test/trajene/Run.trajene
Hunk #1 FAILED at 26.
1 out of 1 hunk FAILED -- saving rejects to file
test/trajene/Run.trajene.rej
patching file test/trajene/trajene.in
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
test/trajene/trajene.in.rej
patching file test/trajene/trajene.out.save
Reversed (or previously applied) patch detected! Skipping patch.
110 out of 110 hunks ignored -- saving rejects to file
test/trajene/trajene.out.save.rej
patching file src/ncsu-umbrella-slice/configure
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
src/ncsu-umbrella-slice/configure.rej
patching file src/ncsu-umbrella-slice/cox308-netCDF.m4
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
src/ncsu-umbrella-slice/cox308-netCDF.m4.rej
patching file src/sander/qmmm_module.f
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file
src/sander/qmmm_module.f.rej
patching file src/sander/qm2_load_params_and_allocate.f
Reversed (or previously applied) patch detected! Skipping patch.
*
I do not know how to solve these problems. Can somebody help me with this?
with regards,
Anogna
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Received on Wed Dec 05 2012 - 00:00:02 PST
