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.
Eric
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/vnd.palm attachment: ADA.pdb
Received on Tue Mar 23 2010 - 03:30:02 PDT
