Dear list,
I used in the past the command "solvatecap" to solvate only the ligand in a
protein/ligand complex.
With "solvatecap" it is possible to specify the position of the center of
the sphere in the 3rd argument:
solvatecap solute solvent position radius
To specify the position I use the following syntax:
lig = loadpdb ligand.pdb
prot = loadpdb protein.pdb
complex = combine {prot lig}
solvatecap complex TIP3PBOX complex.199 15.0 (where 199 is the residue
number of the ligand in the complex)
I would like to try "solvetashell" for different reasons. Since
"solvateshell" is not a sphere, the only argument to position the shell is
with the 1st argument:
solvateshell solute solvent radius
Solute should be UNIT.
When I use "solvateshell", the coordinates of the ligand and the water
molecules are changed from the origin so the ligand doesn't bind anymore in
the active site.
lig = loadpdb ligand.pdb
prot = loadpdb protein.pdb
solvatecap lig TIP3PBOX 15.0
complex = combine {prot lig}
How is it possible to solvate only the ligand in the complex using the
command "solvateshell"?
ps: I am using AMBER v8.0
Thanks for your help.
Pascal
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Received on Sun Oct 01 2006 - 06:07:16 PDT
