AMBER Archive (2006)

Subject: AMBER: problem to center solvateshell

From: Bonnet, Pascal [PRDBE] (PBONNET_at_PRDBE.JNJ.COM)
Date: Fri Sep 29 2006 - 04:30:49 CDT

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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