[gmx-users] LIGAND ERRORS

Raj Badhan r.k.badhan at stud.man.ac.uk
Mon Dec 15 22:49:01 CET 2003

Dear ALL,
I've tried running simulations using my ligand-protein complex and 
initially with the drug-receptor tutorial from dr. kerrigan.
However, each time I solvate the box, the create a box , its size is 

 system size :103.000  3.861  4.761 (nm)

and when I solvate and check GRO file in VMD, the protein is 
solvated within the box, but the ligand is stretched with no bonds 
connecting it, outside of the box.

These are all done using the windows ported version of gromacs.
I've done exactly what has been stated in dr kerrigans tutorial, but 
keep getting this sort of error.
Any suggestions would be appreciated.
Raj Badhan
Postgraduate researcher
School of Pharmacy and Pharmacetical Science
The University of Manchester
Manchester, UK.

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