[gmx-users] LIGAND ERRORS
r.k.badhan at stud.man.ac.uk
Mon Dec 15 22:49:01 CET 2003
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.
School of Pharmacy and Pharmacetical Science
The University of Manchester
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