[gmx-users] solvate protein in water?

Zhen Qin zhen at hec.utah.edu
Thu Oct 27 00:39:58 CEST 2005

 I met a problem with solvating my protein inside water molecules.
 My protein is inside a triclinic box (with alpha=90, belta=90, and 
garma=60), and the box-vectors satisfy the GROMACS' requirements.  I use 
"genbox -cp protein.pdb -cs spc216.gro -o out.pdb". But I found in 
out.pdb, the box's shape has been changed to cubic. That is not what 
I've expected. I have hoped that water molecules are added to the 
triclinic box and solvate the protein. In genbox's options, the "vector" 
option is only for the length of each box's vector, not including the 
angles. How could I specify the angle?
Is there any way to solvate a protein in a non-cubic box?

Thanks alot.


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