[AMBER] Solvatebox on Amber8

From: pellegrini <pellegrini.ill.fr>
Date: Tue, 23 Mar 2010 11:29:32 +0100

Hello everybody,

I am using Amber 8 with tleap program in order to generate top and crd
file for a protein with a sugar-ligand.
Using glycam 06 I could generate successfully the top and crd for the
solute but I went into troubles when solvating my system. Indeed, using
the following commands on the attached PDB file:

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

creates a box that first is not cubic at all and second does not
surround my ligand like I would expect.

Going back to the roots by trying:

source leaprc.ff99
solvatebox ACE 20
savepdb ace ace.pdb

also provides a box that is not cubic at all.

Is there something that I am not doing correctly with those commands ?

thank you very much in advance for your help.


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Received on Tue Mar 23 2010 - 03:30:02 PDT
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