> PTRAJ: donor mask :1-54.O
> Mask [:1-54.O] represents 54 atoms
>
> PTRAJ: acceptor WAT O H1
>
> PTRAJ: acceptor WAT O H2
....
> Estimated memory usage for this hbond call: 1986.48 MB
> donors: 54 acceptors: 1604
The estimated memory usage for this command is 2GB of RAM. Likely your
machines cannot handle this...
> Processing AMBER restart file ../col.crd
> ERROR in safe_malloc: Error in alloc of 693274464 bytes
(error allocating ~700MB of memory)
I would suggest using the solventacceptor command instead as this has
significantly less of a memory footprint since only waters close to the
donor atoms are tracked.
In the script you sent, remove the acceptor commands. Also, I would
increase the solventneighbor to be something like 6.
Finally, the grid command used
grid grid.list 8 3.0 8 3.0 24 3.0 :WAT max 0.8
is not recommended since it is too coarse (only covering a 24A grid
around your center). I normally use
grid grid.list 100 0.5 100 0.5 100 0.5 :WAT.O
....however, for this to have any meaning (i.e. the grid of atom counts),
the structures have to be fit to a common reference frame. So, do an RMS
fit to the first frame about the region of interest. If you do the whole
molecule (:1-54) motion may blur the grid occupancy.
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Received on Fri Oct 21 2005 - 03:53:00 PDT
