[AMBER] Problem with solvationbox command

From: pellegrini <pellegrini.ill.fr>
Date: Tue, 23 Mar 2010 14:11:17 +0100

Hello evrybody,

I justed posted a few hours ago about a problem encountered when
solvating a protein with a
sugar-ligand. Sorry, but in my previous post, I was perhaps too fuzzy.

Using the following commands on the first attached PDB file (ADA.pdb):

source leaprc.ff99
source leaprc.Glycam_06
x = loadPDB ADA.pdb
solvateBox x TIP3PBOX 10.0
addions x Na+ 0
saveAmberParm x ADA_Solvated.top ADA_Solvated.crd
savePDB x ADA_Solvated.pdb

creates a weird solvation box that does not surround the solute at all
as you can see when looking at the second attached file
(ADA_Solvated.pdb). Would you have any clue of what is (or I did) wrong
with my setup ?

thank you very much

Eric



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Received on Tue Mar 23 2010 - 06:30:02 PDT
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