[Dock-fans] amberize_ligand

Scott Brozell sbrozell at scripps.edu
Tue Mar 6 10:02:58 PST 2007


Hi,

On Mon, 26 Feb 2007, Gustavo HMF Souza wrote:

> How can I fix this error? Someone ca explain me how to do this?
>
>  korax at cf1n01 bin]$ ./amberize_ligand nobppnepripar5rigid_ranked.1 -c gas
> Using ligand file prefix: nobppnepripar5rigid_ranked.1
> Using total charge: -c
> Using antechamber options: -c gas

Unfortunately, there is a charge related error in the script.
In addition, the documentation is out of sync.
A patch is to always specify the charge, i.e., try this:
./amberize_ligand nobppnepripar5rigid_ranked.1 0 -c gas
                                              ^^^

> running: antechamber to generate GAFF mol2 file format with AM1-BCC
> charges
> The atom number exceeds the MAXATOM, reallocate memoryRunning:
> /home2/cluster/proj/proj379/korax/dock6/bin/bondtype -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full
>
> Info: the atom number exceeds the MAXATOM, reallocate memory
> automatically
> 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 "/home2/cluster/proj/proj379/korax/dock6/bin/bondtype
> -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full"
> in judgebondtype() of antechamber.c properly, exit

The above probably will not eliminate this antechamber issue.
If so then you can perform step (1).
Send me the ligand input file if problems remain.


> Cannot open file nobppnepripar5rigid_ranked.1.gaff.mol2, exit
> -I: Adding /home2/cluster/proj/proj379/korax/dock6/parameters/leap/prep
> to search path.
> -I: Adding /home2/cluster/proj/proj379/korax/dock6/parameters/leap/lib to
> search path.
> -s: Ignoring startup file: leaprc
> -f: Source /tmp/._amberize_ligand.leapin.16840.

LEaP fails because antechamber fails.  We are planning to improve
the robustness of the amber score preparation.

Scott



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