[Dock-fans] out of memory mallocing in PBSA

Prashant Kumar prashantkbio at gmail.com
Mon Jun 2 05:18:09 PDT 2008

Dear Dock Fans ,
                               I am using DOCK6.1 with zap for MM-PBSA
calculation . While performing the docking in rigid manner I am getting good
results with no problem , but in other hand  for flexible one I am getting
following  error .

Initializing Library File Routines...
Initializing Conformer Generator Routines...
Initializing PB/SA Score Routines...
Initializing Grid Score Routines...
 Reading the energy grid from /home/prashant/olddock/1KZK/3_grid/grid1.nrg
out of memory mallocing  31786900 for Eps.x!

Total oe_memory currently allocated=        0.552148 Mbytes
Total oe_object_memory currently allocated= -1245.293528 Mbytes
Total memory currently allocated=           -1244.741380 Mbytes
*******pointer/memory list*******
pointer -1235980280 has 262144 bytes of memory
pointer -1236246520 has 262144 bytes of memory
pointer 155365656 has 200 bytes of memory
pointer 155365864 has 40 bytes of memory
pointer -1142946712 has 1000 bytes of memory
pointer 156516616 has 26620 bytes of memory
 and bla bla bla (thousand of lines )

I want to clear one thing in my case rigid docking is not possible . I also
did some things with ulimit unix command but nothing worked out . Please
give me some suggestion to rectify this problem .

Prashant kumar
Centre For Computational Biology and Bioinformatics
Jawaharlal Nehru University
New Delhi 110067
prashantkumar at mail.jnu.ac.in , prashantkbio at gmail.com
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