Dear AMBER List,
I've just upgraded to AMBER 11 and trying to perform MM-PBSA
calculations. Unfortunately, it seems that pbsa is compiled incorrectly:
tests say something like following:
==============================================================
cd sander_pbsa_dmp && ./Run.dmp.min
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander 083E3947 Unknown Unknown Unknown
sander 080FA517 Unknown Unknown Unknown
sander 080CBCCA Unknown Unknown Unknown
sander 080CABAB Unknown Unknown Unknown
sander 0804F244 Unknown Unknown Unknown
libc.so.6 40989C0E 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 083E3947 Unknown Unknown Unknown
sander 080FA517 Unknown Unknown Unknown
sander 080CBCCA Unknown Unknown Unknown
sander 080CABAB Unknown Unknown Unknown
sander 0804F244 Unknown Unknown Unknown
libc.so.6 40989C0E 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 083E3947 Unknown Unknown Unknown
sander 080FA517 Unknown Unknown Unknown
sander 080CBCCA Unknown Unknown Unknown
sander 080CABAB Unknown Unknown Unknown
sander 0804F244 Unknown Unknown Unknown
libc.so.6 40989C0E 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 083E3947 Unknown Unknown Unknown
sander 080FA517 Unknown Unknown Unknown
sander 080CBCCA Unknown Unknown Unknown
sander 080CABAB Unknown Unknown Unknown
sander 0804F244 Unknown Unknown Unknown
libc.so.6 40989C0E Unknown Unknown Unknown
./Run.lsolver.min: Program error
make[1]: [test.pbsa] Error 1 (ignored)
cd sander_pbsa_radi && ./Run.ion.min
diffing ./out.save/Li.out.save with Li.out
PASSED
==============================================================
I use Intel compilers (composerxe-2011.2.137) on 32-bit machine. What
can I do to beat this error?
Best regards,
Dmitry
--
Dmitry Osolodkin
Researcher
Group of Computational Molecular Design
Department of Chemistry
Moscow State University
Moscow 119991 Russia
e-mail: dmitry_o.qsar.chem.msu.ru
Phone: +7-495-9393557
Fax: +7-495-9390290
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Received on Tue Apr 19 2011 - 06:00:02 PDT
