Re: [AMBER] _mmpbsa_py_energy error durint PB calculations from Jason Swails on 2011-08-16 (Amber Archive Aug 2011)

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 16 Aug 2011 07:20:48 -0400

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
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Received on Tue Aug 16 2011 - 04:30:04 PDT