AMBER Archive (2009)

Subject: Re: [AMBER] saquinavir parameterization with antechamber

From: Oliver Kuhn (oak_at_gmx.org)
Date: Thu Jul 23 2009 - 02:02:49 CDT

-------- Original-Nachricht --------
> Datum: Wed, 22 Jul 2009 20:41:21 +0200
> Von: FyD <fyd_at_q4md-forcefieldtools.org>
> An: amber_at_ambermd.org
> Betreff: Re: [AMBER] saquinavir parameterization with antechamber

> Dear Oliver,
>
> It looks like you have no hydrogen in your PDB file. Add the missing
> hydrogens & try again.
>
> regards, Francois

>
>
> > 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
> > 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.
Thank you, Francois.
After adding hydrogens with open babel, divcon runs a long time (and doesn't stop). When I switch to resp charges, its the same.
How long should a resp or am1 calculation take for my molecule?

> > Then I thought: hey, you got a mol2 from pdb2pqr and took this as input.
What about this case:
> >
> > $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
> > 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
> > regards
> > Oliver
>
>
>
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