[Dock-fans] out of memory mallocing in PBSA

Scott Brozell sbrozell at scripps.edu
Tue Jun 3 13:30:09 PDT 2008


Hi,

Upgrade to DOCK 6.2; a PBSA score memory leak was fixed in 6.2.

Thanks to Diana Roe and Terry Lang for noticing this.
Scott

On Mon, 2 Jun 2008, Scott Brozell wrote:

> On Mon, 2 Jun 2008, Prashant Kumar wrote:
> 
> >                                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!
> 
> The last message is from the ZAP library.
> 
> 
> > *******
> > 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
> 
> The negative values suggest that something has overflowed.
> 
> 
> > 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 .
> 
> The general recipe for these resource exhaustion situations is to
> benchmark your system: start with a small calculation (small grid,
> small receptor, ...) and systematically increase its size.
> Eventually, you will develop a memory consumption model as a function
> of the various independent variables above (grid size, ...).
> 
> Get rich quick schemes involve doing some arithmetic
> (how much total memory on your platform, how much available memory,
> how big are the grid files) in the hopes finding a big memory sink
> or trying a different platform in the hopes of finding more resources.
> 
> Look at threads involving Francesco Pietra over the last few months
> for other tidbits.
> 
> Good luck,
> Scott




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