Re: [AMBER] error preparing a ligand using antechamber

From: Paul Rigor <paul.rigor.uci.edu>
Date: Mon, 16 May 2011 16:45:40 -0700

Hello again,

I just wanted to include additional information when running antechamber
directly and teasing out the actual binary that it calls. Below is the
warning message from 'bondtype'

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

So I edited antechamber/define.h to raise the PSCUTOFF value to 100 (from
10) and recompiled ambertools. However, I still receive the same error
message.

Has anyone encountered this before? The structure shouldn't have any
incorrect connectivities.

THanks,
Paul 
--
Paul Rigor
http://www.ics.uci.edu/~prigor
On Mon, May 16, 2011 at 2:18 PM, Paul Rigor <paul.rigor.uci.edu> wrote:
> Hi,
>
> 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'.
>
> Thanks!
> Paul
>
> ==BEGIN ERROR==
>
> Chain-initial residues that are actual N terminii:
> Chain-initial residues that are not actual N terminii:
> Chain-final residues that are actual C terminii:
> Chain-final residues that are not actual C terminii:
> 0 hydrogen bonds
> Hydrogens added
> Charge model: AMBER ff99SB
> Assigning partial charges to residue LIG (net charge +0) with am1-bcc
> method
> Running ANTECHAMBER command: C:/Program Files/Chimera
> 1.5.3rc/bin/amber11/bin\antechamber -ek qm_theory='AM1', grms_tol=0.02,
> tight_p_conv=0, scfconv=1.d-10, -i
> c:\users\family\appdata\local\temp\tmpk4hkse\ante.in.mol2 -fi mol2 -o
> c:\users\family\appdata\local\temp\tmpk4hkse\ante.out.mol2 -fo mol2 -c bcc
> -nc 0 -j 5 -s 2
> (LIG)
>
> (LIG)
>
> (LIG) Total number of electrons: 296; net charge: 0
>
> (LIG)
>
> (LIG) Running: "C:/Program Files/Chimera 1.5.3rc/bin/amber11/bin/sqm" -O -i
> sqm.in -o sqm.out
>
> (LIG) Error: cannot run ""C:/Program Files/Chimera
> 1.5.3rc/bin/amber11/bin/sqm" -O -i sqm.in -o sqm.out" of bcc() in charge.c
> properly, exit
>
> (LIG) Running: "C:/Program Files/Chimera 1.5.3rc/bin/amber11/bin/bondtype"
> -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> (LIG)
>
> (LIG) Running: "C:/Program Files/Chimera 1.5.3rc/bin/amber11/bin/atomtype"
> -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
>
> Failure running ANTECHAMBER for residue LIG
> Check reply log for details
> --
> Paul Rigor
> http://www.ics.uci.edu/~prigor
>
>
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Received on Mon May 16 2011 - 17:00:02 PDT
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