AMBER Archive (2009)

Subject: [AMBER] saquinavir parameterization with antechamber

From: Oliver Kuhn (
Date: Wed Jul 22 2009 - 10:42:49 CDT

Hi ambers,

I tried to parameterize saquinavir in two ways described in tutorials and always got stuck somewhere.

Trial 1 (based on basic tutorial 4 - - 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
Running: /usr/local/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full

Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C
(4) increase PSCUTOFF in define.h and recompile bondtype.C
    Be cautious, use a large value of PSCUTOFF (>10) will significantly increase the computer time
Error: cannot run "/usr/local/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of antechamber.c properly, exit

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.
Then I thought: hey, you got a mol2 from pdb2pqr and took this as input.

$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 -fo mol2 -c bcc -s 2

ran through fine without any warning, - again 'ATTN, need revision'

Trial 2 (based on

antechamber -fi mol2 -fo gcrt -i lig.pdb2pqr.mol2 -o lig.gau
antechamber -fi gout -fo prepi -i lig.gau -o lig_resp_amber.prepi -c resp -j both -at amber -rn lig

Then antechamber begins to run for hours and hours with no message!?

Saquinavir-complexes have been simulated with amber very often.
Can anybody tell me where the problem is?

Help appreciated

  • chemical/x-pdb attachment: lig.pdb

AMBER mailing list