Thank you Jason.
I ran AT15_Amber11.py. Errors reported in Amber 11 test.log but not included
in the result of AT15_Amber11.py are as follows;
Run.dmp.min, Run laz6.min, Run.ion.min, and Run.pbsa_decpw.
Test.log for AmberTools report some more errors. Those are
Run.IIM.min, Run.t4bnz.min., and Run.mb., not included in
AT15_Amber11.py-result.
My OS is Scientific Linux 6.0 and I compiled Amber11 and AmberTools with
Intel compiler 12.0.2.137 for 64bit.
Hiromichi
2011/8/16 Jason Swails <jason.swails.gmail.com>
> Run AT15_Amber11.py. At the bottom of that, it should give a summary about
> which tests are *expected* to fail, specifically using sander and PBSA.
> The
> reason this occurs is because the pbsa program was updated and the user
> interface slightly changed (for instance, with different input namelist
> variables), which causes some tests to quit in error (like you saw) and
> other tests to fail with what appear to be non-trivial roundoff error, but
> the numbers are fairly close regardless.
>
> As long as all of the AmberTools tests pass and *only* those tests listed
> by
> AT15_Amber11.py fail, you should be fine.
>
> Hope this helps,
> Jason
>
> On Tue, Aug 16, 2011 at 12:36 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>
> > Interesting ... is there any other error messages when you run rest of
> > the test cases? There is a makefile to run all these test cases under
> > the test directory. It is crucial that all test cases pass after your
> > installation.
> >
> > All the best,
> > Ray
> >
> > 2011/8/15 鶴井博理 <tsurui.juntendo.ac.jp>:
> > > Thank you Jason.
> > >
> > > I noticed that sander_pbsa was also occurred in test.
> > > Below is the output of the test log.
> > > I found *Dmitry Osolodkin in 19, April 2011 also suffered form this
> > error,
> > > and I tired to obtain informations about this issue*, but the link in
> > this
> > > thread did not work.
> > > Could you give me any suggestion?
> > >
> > >
> > > ======cd sander_pbsa_dmp && ./Run.dmp.min
> > > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > > Image PC Routine Line
> > > Source
> > > sander 00000000008241E3 Unknown Unknown
> > Unknown
> > > sander 00000000004C81A4 Unknown Unknown
> > Unknown
> > > sander 00000000004918C0 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F8F9DFADC5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.dmp.min: Program error
> > > make[1]: [test.pbsa] Error 1 (ignored)
> > > cd sander_pbsa_ipb2 && ./Run.110D.min
> > > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > > Image PC Routine Line
> > > Source
> > > sander 00000000008241E3 Unknown Unknown
> > Unknown
> > > sander 00000000004C81A4 Unknown Unknown
> > Unknown
> > > sander 00000000004918C0 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007FD403CBBC5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.110D.min: Program error
> > > make[1]: [test.pbsa] Error 1 (ignored)
> > > cd sander_pbsa_delphi && ./Run.1az6.min
> > > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > > Image PC Routine Line
> > > Source
> > > sander 0000000000824209 Unknown Unknown
> > Unknown
> > > sander 00000000004C81A4 Unknown Unknown
> > Unknown
> > > sander 00000000004918C0 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007FE3FEFB0C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.1az6.min: Program error
> > > make[1]: [test.pbsa] Error 1 (ignored)
> > > cd sander_pbsa_lpb && ./Run.lsolver.min
> > > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > > Image PC Routine Line
> > > Source
> > > sander 00000000008241E3 Unknown Unknown
> > Unknown
> > > sander 00000000004C81A4 Unknown Unknown
> > Unknown
> > > sander 00000000004918C0 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F67BC627C5D Unknown Unknown
> > Unknown
> > > sander
> > 0========================================================
> > > diffing save/work.txt with work.txt
> > > PASSED
> > >
> > > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > > Image PC Routine Line
> > > Source
> > > sander 00000000008241E3 Unknown Unknown
> > Unknown
> > > sander 00000000004C81A4 Unknown Unknown
> > Unknown
> > > sander 00000000004918C0 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F6036FF1C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.ion.min: Program error
> > > make[1]: [test.pbsa] Error 1 (ignored)
> > > cd sander_pbsa_tsr && ./Run.tsrb.min
> > > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > > Image PC Routine Line
> > > Source
> > > sander 00000000008241E3 Unknown Unknown
> > Unknown
> > > sander 00000000004C81A4 Unknown Unknown
> > Unknown
> > > sander 00000000004918C0 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F1DA2CB2C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.tsrb.min: Program error
> > > make[1]: [test.pbsa] Error 1 (ignored)
> > > cd sander_pbsa_frc && ./test
> > > dbf_0.argasp
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file
> /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_0/argasp/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F13EA4DFF6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F13EA4DEAE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F13EAD69E12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F13EACDF5CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F13EACDECDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F13EAD20C62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F13E9F52C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.argasp.min: Program error
> > > dbf_0.dadt
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_0/dadt/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F8030891F6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F8030890AE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F803111BE12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F80310915CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F8031090CDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F80310D2C62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F8030304C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.dadt.min: Program error
> > > dbf_0.dgdc
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_0/dgdc/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F9076F33F6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F9076F32AE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F90777BDE12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F90777335CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F9077732CDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F9077774C62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F90769A6C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.dgdc.min: Program error
> > > dbf_0.lysasp
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file
> /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_0/lysasp/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F9C12B73F6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F9C12B72AE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F9C133FDE12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F9C133735CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F9C13372CDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F9C133B4C62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F9C125E6C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.lysasp.min: Program error
> > > dbf_0.polyALA
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file
> > /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_0/polyALA/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F7A6766FF6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F7A6766EAE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F7A67EF9E12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F7A67E6F5CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F7A67E6ECDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F7A67EB0C62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F7A670E2C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.polyALA.min: Program error
> > > dbf_0.polyAT
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file
> /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_0/polyAT/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007FA11ACBAF6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007FA11ACB9AE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007FA11B544E12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007FA11B4BA5CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007FA11B4B9CDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007FA11B4FBC62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007FA11A72DC5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.polyAT.min: Program error
> > > dbf_1.argasp
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file
> /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_1/argasp/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F5C219AAF6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F5C219A9AE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F5C22234E12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F5C221AA5CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F5C221A9CDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F5C221EBC62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F5C2141DC5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.argasp.min: Program error
> > > dbf_1.dadt
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_1/dadt/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F233F822F6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F233F821AE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F23400ACE12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F23400225CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F2340021CDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F2340063C62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F233F295C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.dadt.min: Program error
> > > dbf_1.dgdc
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_1/dgdc/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F0132D7DF6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F0132D7CAE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F0133607E12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F013357D5CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F013357CCDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F01335BEC62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F01327F0C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.dgdc.min: Program error
> > > dbf_1.lysasp
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file
> /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_1/lysasp/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F287ED26F6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F287ED25AE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F287F5B0E12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F287F5265CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F287F525CDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F287F567C62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F287E799C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.lysasp.min: Program error
> > > dbf_1.polyALA
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file
> > /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_1/polyALA/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F88D6D5AF6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F88D6D59AE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F88D75E4E12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F88D755A5CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F88D7559CDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F88D759BC62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F88D67CDC5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.polyALA.min: Program error
> > > dbf_1.polyAT
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file
> /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_1/polyAT/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F3A327CBF6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F3A327CAAE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F3A33055E12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F3A32FCB5CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F3A32FCACDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F3A3300CC62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F3A3223EC5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.polyAT.min: Program error
> > > dbf_2.argasp
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file
> /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_2/argasp/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007FEC12781F6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007FEC12780AE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007FEC1300BE12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007FEC12F815CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007FEC12F80CDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007FEC12FC2C62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007FEC121F4C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.argasp.min: Program error
> > > dbf_2.dadt
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_2/dadt/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F7A46520F6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F7A4651FAE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F7A46DAAE12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F7A46D205CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F7A46D1FCDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F7A46D61C62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F7A45F93C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.dadt.min: Program error
> > > dbf_2.dgdc
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_2/dgdc/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F8E667CFF6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F8E667CEAE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F8E67059E12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F8E66FCF5CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F8E66FCECDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F8E67010C62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F8E66242C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.dgdc.min: Program error
> > > dbf_2.lysasp
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file
> /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_2/lysasp/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F838B35CF6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F838B35BAE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F838BBE6E12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F838BB5C5CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F838BB5BCDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F838BB9DC62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F838ADCFC5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.lysasp.min: Program error
> > > dbf_2.polyALA
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file
> > /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_2/polyALA/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F4C06F8FF6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F4C06F8EAE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F4C07819E12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F4C0778F5CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F4C0778ECDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F4C077D0C62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F4C06A02C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.polyALA.min: Program error
> > > dbf_2.polyAT
> > > forrtl: severe (19): invalid reference to variable in NAMELIST input,
> > unit
> > > 5, file
> /home/tsurui/Downloads/amber11/test/sander_pbsa_frc/dbf_2/polyAT/
> > > min.in, line 10, position 29
> > > Image PC Routine Line
> > > Source
> > > libintlc.so.5 00007F9559C11F6A Unknown Unknown
> > Unknown
> > > libintlc.so.5 00007F9559C10AE5 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F955A49BE12 Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F955A4115CB Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F955A410CDE Unknown Unknown
> > Unknown
> > > libifcore.so.5 00007F955A452C62 Unknown Unknown
> > Unknown
> > > sander 000000000081BDEC Unknown Unknown
> > Unknown
> > > sander 00000000004BA166 Unknown Unknown
> > Unknown
> > > sander 0000000000490718 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F9559684C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.polyAT.min: Program error
> > > cd sander_pbsa_decres && ./Run.pbsa_decres
> > > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > > Image PC Routine Line
> > > Source
> > > sander 00000000008241E3 Unknown Unknown
> > Unknown
> > > sander 00000000004C81A4 Unknown Unknown
> > Unknown
> > > sander 00000000004918C0 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007F063AD3FC5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.pbsa_decres: Program error
> > > make[1]: [test.pbsa] Error 1 (ignored)
> > > cd sander_pbsa_decpw && ./Run.pbsa_decpw
> > > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > > Image PC Routine Line
> > > Source
> > > sander 00000000008241E3 Unknown Unknown
> > Unknown
> > > sander 00000000004C81A4 Unknown Unknown
> > Unknown
> > > sander 00000000004918C0 Unknown Unknown
> > Unknown
> > > sander 0000000000490528 Unknown Unknown
> > Unknown
> > > sander 00000000004030BC Unknown Unknown
> > Unknown
> > > libc.so.6 00007FE0A8648C5D Unknown Unknown
> > Unknown
> > > sander 0000000000402FB9 Unknown Unknown
> > Unknown
> > > ./Run.pbsa_decpw: Program error
> > > make[1]: [test.pbsa] Error 1 (ignored)
> > > cd cnstph && ./Run.cnstph
> > > diffing mdout.save with mdout
> > > PASSED
> > >
> > >
> > > 2011/8/14 Jason Swails <jason.swails.gmail.com>
> > >
> > >> I don't see any error messages actually printed out by the program
> (the
> > >> mmpbsa_py_energy program, not MMPBSA), so it's hard to assess what
> went
> > >> wrong.
> > >>
> > >> Did you make any changes to any of the files from the tutorial before
> > >> running it?
> > >>
> > >> Thanks!
> > >> Jason
> > >>
> > >> On Sun, Aug 14, 2011 at 7:30 AM, HIromichi Tsurui <
> > tsurui.juntendo.ac.jp
> > >> >wrote:
> > >>
> > >> > Hi all,
> > >> > I would like to calculate receptor-ligand interaction energy by
> > >> > MMPBSA/GBSA.
> > >> > I tried to do so using Tutorial Advanced 3, Ras-raf model. Energy
> > >> > calculation by GB seems to go well.
> > >> > However, mmpbsa_py_energy error occurred during PB calculations.
> > >> > Could anyone suggest me what happened and how should I do?
> > >> >
> > >> >
> > >> >
> > >> > $ MMPBSA -O -i mmpbsa_1b.in -o FINAL_RESULTS_MMPBSA.dat -sp
> > >> > ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp
> > raf.prmtop
> > >> -y
> > >> > prod.mdcrd
> > >> > Reading command-line arguments and input files...
> > >> > Loading and checking parameter files for compatibility...
> > >> > ptraj found! Using /home/tsurui/Downloads/amber11/bin/ptraj
> > >> > mmpbsa_py_energy found! Using
> > >> > /home/tsurui/Downloads/amber11/bin/mmpbsa_py_energy for GB
> > calculations
> > >> > mmpbsa_py_energy found! Using
> > >> > /home/tsurui/Downloads/amber11/bin/mmpbsa_py_energy for PB
> > calculations
> > >> > Preparing trajectories for simulation...
> > >> > 50 frames were read in and processed by ptraj for use in
> calculation.
> > >> >
> > >> > Beginning GB calculations with mmpbsa_py_energy...
> > >> > calculating complex contribution...
> > >> > calculating receptor contribution...
> > >> > calculating ligand contribution...
> > >> >
> > >> > Beginning PB calculations with mmpbsa_py_energy...
> > >> > calculating complex contribution...
> > >> > PB Info in pb_read(): npopt has been overwritten with inp
> > >> > Error: mmpbsa_py_energy error during PB calculations!
> > >> > NOTE: All files have been retained for debugging purposes. Type
> > MMPBSA.py
> > >> > --clean to erase these files.
> > >> >
> > >> >
> > >> > << _MMPBSA_complex_pb.mdout >>
> > >> > Reading parm file (ras-raf.prmtop)
> > >> > title:
> > >> >
> > >> > mm_options: e_debug=3
> > >> > mm_options: ipb=1
> > >> > mm_options: inp=1
> > >> > mm_options: epsin=1.000000
> > >> > mm_options: epsout=80.000000
> > >> > mm_options: smoothopt=0
> > >> > mm_options: istrng=100.000000
> > >> > mm_options: radiopt=0
> > >> > mm_options: dprob=1.400000
> > >> > mm_options: iprob=2.000000
> > >> > mm_options: npbopt=0
> > >> > mm_options: solvopt=1
> > >> > mm_options: accept=0.001000
> > >> > mm_options: maxitn=1000
> > >> > mm_options: fillratio=4.000000
> > >> > mm_options: space=0.500000
> > >> > mm_options: nfocus=2
> > >> > mm_options: fscale=8
> > >> > mm_options: bcopt=5
> > >> > mm_options: eneopt=2
> > >> > mm_options: cutnb=0.000000
> > >> > mm_options: sprob=1.400000
> > >> > mm_options: cavity_surften=0.005420
> > >> > mm_options: cavity_offset=-1.008000
> > >> > Processing ASCII trajectory (_MMPBSA_complex.mdcrd)
> > >> >
> > >> > Processing frame 1
> > >> > iter Total bad vdW elect nonpolar EPB
> > >> > frms
> > >> >
> > >> >
> > >> >
> > >> > _______________________________________________
> > >> > AMBER mailing list
> > >> > AMBER.ambermd.org
> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >
> > >>
> > >>
> > >>
> > >> --
> > >> Jason M. Swails
> > >> Quantum Theory Project,
> > >> University of Florida
> > >> Ph.D. Candidate
> > >> 352-392-4032
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Aug 16 2011 - 18:00:02 PDT
