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
>>
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Aug 15 2011 - 22:00:03 PDT
