AMBER Archive (2009)

Subject: Re: [AMBER] saquinavir parameterization with antechamber

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Jul 22 2009 - 13:41:21 CDT

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.
> 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
> 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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