AMBER Archive (2005)

Subject: AMBER: mm_pbsa example doesn't run

From: Yuuki Komata (komata_at_glyco.sci.hokudai.ac.jp)
Date: Fri Jan 21 2005 - 06:10:48 CST

Dear Ambers,

   I am going to perform MM-PBSA simulations with AMBER 8 on
IBM aix 5.2 and SUNOS 5.9. Compiles were O.K., and test run good.
But the problem is I can't run Example programs for MM_PBSA in
$AMBERMOHE/src/mm_pbsa/Examples.

1 On IBM aix, there is only the result of the first step of run in
ras_raf_II_wt_com.all.out
MM
GB
PB
MS
1
 BOND = 693.4575 ANGLE = 1895.7111 DIHED = 1478.8198
 VDWAALS = -1974.0288 EEL = -17194.5212 EGB = -3760.0843
 1-4 VDW = 866.5634 1-4 EEL = 7173.9328 RESTRAINT = 0.0000

and the last of the pbsa_com.1.out is the message
PB bomb in pb_init(): Allocation aborted 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0

and in the mm_pbsa.log, it seems the program stopped at calculationg the
part of pbsa.

2 On SUNOS 5.9, there are two results written in ras_raf_II_wt_com.all.out;
MM
GB
PB
MS
1
 BOND = 693.4575 ANGLE = 1895.7111 DIHED = 1478.8198
 VDWAALS = -1974.0288 EEL = -17194.5212 EGB = -3760.0843
 1-4 VDW = 866.5634 1-4 EEL = 7173.9328 RESTRAINT = 0.0000
corrected reaction field energy: -5727.880064
surface area = 12597.987
2
 BOND = 702.5472 ANGLE = 1864.7257 DIHED = 1470.3932
 VDWAALS = -1971.3785 EEL = -17225.7579 EGB = -3784.7259
 1-4 VDW = 858.8716 1-4 EEL = 7254.3905 RESTRAINT = 0.0000

and pbsa_com.1.out is stopped at the message;
Number of triangulated 3-point waters found: 0

and as in the case of IBM aix 5.2, the last message of mm_pbsa.log is 'Calc PBSA'.

  I looked up the amber 8 bugfixes and patched bugfix 4 and 27 related to pbsa
following recompile, but the runs went bad. Does anyone encounterd this problem?
Does anybody know what is wrong and how to fix?

  Thank you in advance. Have a nice weekend.

Yuuki A. Komata, Ph. D. Eng.
komata_at_glyco.sci.hokudai.ac.jp
Fax & Phone : +81-11-706-9038
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu