Re: [AMBER] error preparing a ligand using antechamber

From: Paul Rigor <paul.rigor.uci.edu>
Date: Mon, 16 May 2011 17:31:11 -0700

Hi,

I've attached the correct file here. 'reduce' didn't reduce the carbonyls,
which is good. But the rest of the steps, specifically, determining the
bondtype, does not proceed. I've also recompiled antechamber/define.h with
#define PSCUTOFF 100.

Thanks,
Paul

==Messages below==
antechamber -i lycopenepdb_h.pdb -fi pdb -o lycopenepdb_h.mol2 -fo mol2 -c
bcc -s 2
Running: /tools/amber/AmberTools/1.5/amber11/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

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 PSCUTOFF in define.h and recompile bondtype.c
    Be cautious, use a large value of PSCUTOFF (>100) will significantly
increase the computation time

Error: cannot run "/tools/amber/AmberTools/1.5/amber11/bin/bondtype -j full
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit 


--
Paul Rigor
http://www.ics.uci.edu/~prigor
On Mon, May 16, 2011 at 5:13 PM, case <case.biomaps.rutgers.edu> wrote:
> On Mon, May 16, 2011, Paul Rigor wrote:
>
> > I was using chimera (Windows/Linux) and then compiled ambertools (Linux)
> > directly for preparing a ligand for docking.  However, I've run into
> > problems adding partial charges. Below is a detailed run from the Chimera
> > log along with a not-so-verbose error message. Any help is appreciated.
> And
> > attached is the molecule I'm working with. I've already attached
> hydrogens
> > to the attached molecule through 'reduce'.
>
> ??? It doesn't appear that any hydrogens have been added, at least not in
> the file lycopene_h.pdb.  Unless lycopene is in reduced HETATM database, it
> won't know how to add hydrogens to it.  Be sure you have a good geometry
> and
> all needed hydrogens before calling sqm.
>
> > 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 PSCUTOFF in define.h and recompile bondtype.c
> >     Be cautious, use a large value of PSCUTOFF (>100) will significantly
> > increase the computation time
>
> This is kind of a misleading message: the error is almost always in the
> input file (i.e. option (1)), and I have never personally seen options (2)
> and (3) to be needed or helpful.
>
> ....dac
>
>
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Received on Mon May 16 2011 - 18:00:03 PDT
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