Dear List,
Recently I have moved from amber9 to amber11. I used to do mmpbsa calculation with no problem, but now using amber11 I am getting the following error and it hangs.
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Use of uninitialized value in concatenation (.) or string at /share/apps/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.
Use of uninitialized value in concatenation (.) or string at /share/apps/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.
Use of uninitialized value in concatenation (.) or string at /share/apps/amber11/src/mm_pbsa/mm_pbsa_createinput.pm line 596.
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When I stop the job by combination key Ctrl+c extra message which prints on the screen is:
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forrtl: error (69): process interrupted (SIGINT)
Image PC Routine Line Source
sander 0000000000444010 Unknown Unknown Unknown
sander 0000000000634744 Unknown Unknown Unknown
sander 00000000004A1D49 Unknown Unknown Unknown
sander 0000000000490D02 Unknown Unknown Unknown
sander 000000000048C60C Unknown Unknown Unknown
sander 0000000000402DEC Unknown Unknown Unknown
libc.so.6 0000003C0021D994 Unknown Unknown Unknown
sander 0000000000402CF9 Unknown Unknown Unknown
/share/apps/amber11/bin/sander -O -i sander_com.in -o sander_com.2.out -c ./snapshot_com.crd.2 -p ./ras-raf.prmtop not successful
For details see: http://ambermd.org/Questions/mm_pbsa.html#mmgbsas_command_not_successful <http://ambermd.org/Questions/mm_pbsa.html#mmgbsas_command_not_successful>
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I searched the archive and seems that other users had the same problem before. Based on one of the messages, I defined INP variable in binding_energy.mmpbsa file. It was working but at the middle of the job it hanged. I have extracted 198 snapshots for each of complex, receptor and ligand. Looking at the output files, only the snapshot_com.all.out and snapshot_rec.all.out were generated and the latter one is not complete. Here is the last few lines for snapshot_com.all.out and snapshot_rec.all.out, respectively:
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198
BOND = 760.4007 ANGLE = 2047.3074 DIHED = 2487.7895
VDWAALS = -1845.6158 EEL = -17222.4349 EGB = -3258.7029
1-4 VDW = 872.1515 1-4 EEL = 8562.4253 RESTRAINT = 0.0000
corrected reaction field energy: -5387.134681
surface area = 13028.335
ECAVITY = 13028.335
EDISPER = 0.0000
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37
BOND = 511.9995 ANGLE = 1306.1487 DIHED = 1738.0072
VDWAALS = -1261.0550 EEL = -11392.4018 EGB = -2740.8744
1-4 VDW = 605.8930 1-4 EEL = 5988.8008 RESTRAINT = 0.0000
corrected reaction field energy: -4537.449028
surface area = 9192.071
ECAVITY = 9192.071
EDISPER = 0.0000
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There is also a file called sander_rec.38.out. I can't figure out why this happens. I appreciate if any suggestion.
Cheers, Siavoush
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Received on Mon Aug 08 2011 - 04:00:03 PDT
