AMBER Archive (2009)
Subject: [AMBER] saquinavir parameterization with antechamber
From: Oliver Kuhn (oak_at_gmx.org)
I tried to parameterize saquinavir in two ways described in tutorials and always got stuck somewhere.
Trial 1 (based on basic tutorial 4 - http://ambermd.org/tutorials/basic/tutorial4/create_prmtop.htm) - everything works fine for the example - my lig.pdb is attached
$AMBERHOME/exe/antechamber -i lig.pdb -fi pdb -o lig.mol2 -fo mol2 -c bcc -s 2
Warning: the assigned bond types may be wrong, please :
I thought: ok, maybe, it doesn't like the HETATM entries and changed them to ATOM. Didn't work. I made it totally lookalike the sustiva.pdb. Didn't work.
$AMBERHOME/exe/parmchk -i lig.pdb2pqr.mol2 -f mol2 -o lig.pdb2pqr.frcmod
'ATTN, need revision' anywhere in the frcmod
OK. Maybe it doesn't like the pdb2pqr.mol2 and has to change something.
$AMBERHOME/exe/antechamber -i lig.pdb2pqr.mol2 -fi mol2 -o lig.ac.mol2 -fo mol2 -c bcc -s 2
ran through fine without any warning, - again 'ATTN, need revision'
Trial 2 (based on http://ambermd.org/antechamber/efz.html)
antechamber -fi mol2 -fo gcrt -i lig.pdb2pqr.mol2 -o lig.gau
Then antechamber begins to run for hours and hours with no message!?
Saquinavir-complexes have been simulated with amber very often.