[gmx-users] More solvent errors!!!

David spoel at xray.bmc.uu.se
Mon Dec 1 16:58:01 CET 2003

On Mon, 2003-12-01 at 16:19, Raj Badhan wrote:
> Dear Users,
> In reply to my previous questions and answers from others with 
> regards to a strange error appearing when solvating my protein, I 
> have carried out the tutorial by Dr Kerrigan on the drug-enzyme 
> complex, and get the same error that I get when running my ATP-
> protein solvations using genbox:
> Will generate new solvent configuration of 19x18x16 boxes
> Generating configuration
> Sorting configuration
> Found 1 molecule type:
>     SOL (   3 atoms): 1181952 residues

it's not a strange error. If the system size estimated by genbox
(roughly 40x40x32 nm) is correct, you're out of memory. Buy more memory
or use another computer.

David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel

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