[gmx-users] What is this??

[David van der Spoel]

Marc Charendoff wrote:
> I've been trying to follow the Enzyme-drug tutorial by
> Kerrigan when I ran into the following:
> 
> My input as per tutorial. . . . 
> 
> 2:/gromacs Marc$ genbox -cp trp2.pdb -cs spc216.gro -o
> trp_b4ion.pdb -p trp.top
> 
> 
> Here is the output . . . .
> 
> Opening library file
> /gromacs/share/gromacs/top/aminoacids.dat
> Opening library file
> /gromacs/share/gromacs/top/atommass.dat
> Opening library file
> /gromacs/share/gromacs/top/vdwradii.dat
> Opening library file
> /gromacs/share/gromacs/top/dgsolv.dat
> #Entries in atommass.dat: 82 vdwradii.dat: 26
> dgsolv.dat: 7
> Reading solute configuration
> S  C  A  M  O  R  G
> Containing 2133 atoms in 251 residues
> Initialising van der waals distances...
> Reading solvent configuration
> "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR.
> 1984"
> solvent configuration contains 648 atoms in 216
> residues
> 
> Initialising van der waals distances...
> Will generate new solvent configuration of 68x64x55
> boxes
> genbox(293) malloc: *** vm_allocate(size=1909243904)
> failed (error code=3)
> genbox(293) malloc: *** error: can't allocate region
> genbox(293) malloc: *** set a breakpoint in
> szone_error to debug
> -------------------------------------------------------
> Program genbox, VERSION 3.3
> Source code file: smalloc.c, line: 137
> 
> Fatal error:
> realloc for atoms_solvt->atom (1909243904 bytes, file
> gmx_genbox.c, line 399, atoms_solvt->atom=0x0x 
> 390000)
> -------------------------------------------------------
> 
> "As Always Your Logic Is Impeccable" (Tuvok)
> : Cannot allocate memory
> 
> 
> Guidance appreciated.

you're out of memory.
You need 2 Gb at least. Check whether the input box size (cryst1 record 
in trp2.pdb) is reasonable.

> 
> Marc
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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