[gmx-users] More solvent errors!!!

Raj Badhan r.k.badhan at stud.man.ac.uk
Mon Dec 1 16:21:00 CET 2003

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
Calculating Overlap...
box_margin = 0.315
Removed 372441 atoms that were outside the box
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 0 molecules, 3547989 charge groups and 3547989 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Fatal error: realloc for nl->gid (56767816 bytes, file 
rc\mdlib\ns.c, line 98, nl->gid=0x0x       0): No such file or directory

I checked the amount of memory requested by the program, and it 
peaked at my max ammount (1.5Gb) before halting.
This seems unusual and strange that it would request soo much 
memory, and similar things occurred running my own protein.
This has been run exactly as stated by Dr Kerrigans' tutorial and 
its baffling me!
Any help would be greatly appreciated!

Raj Badhan
Postgraduate researcher
School of Pharmacy and Pharmacetical Science
The University of Manchester
Manchester, UK.

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