[Dock-fans] FW: obtaining AmberTools12 and/or Amber12?

Scott Brozell sbrozell at rci.rutgers.edu
Fri Aug 22 11:26:48 PDT 2014


On Fri, Aug 22, 2014 at 01:45:47PM -0400, Andrew Schaumberg wrote:
> On 08/22/2014 10:25 AM, David A Case wrote:
> >On Thu, Aug 21, 2014, Andrew Schaumberg wrote:
> >
> >>{request for tarball of AmberTools12.}
> >>Ucsf dock6 dependency, would upgrade if possible. Help appreciated.
> >
> >Can you be more specific?  What aspect of dock is giving you problems?
> >Have you tried using AmberTools13?  What are the problems?
> >The dock-fans mailing list might be able to help.  I'm cc-ing this to Scott
> >Brozell, who probably knows as much as anyone about the dock/amber
> >connection.
> >
> >...regards...dac
> Short story: Amber's divcon missing in AmberTools13.  Is it in AmberTools12?

No, but that is not the source of your problems.

Dock6 does not (yet) use an external AmberTools.
Dock6 uses its own set of Amber tools that are distributed with Dock6.
Unset your AMBERHOME variable when using Dock6:

> Long story:
> `make dock` in DOCK's test/ directory fails in an amber test.
> >make[1]: Entering directory
> >'/home/a-day/bin/dock/dock6/install/test/amber_score_181l'
> >../../../bin/prepare_amber.pl lig.mol2 181l.pdb
> >Coordinate and parameter files for the Receptor 181l generated.
> >The AMBER score tagged mol2 file lig.amber_score.mol2 generated.
> >Splitting the multiple Ligand mol2 file into single mol2 files.
> >The single mol2 files will have the prefix: lig
> >The number of single Ligand mol2 files generated is 1.
> >Generating coordinate and parameter files for Ligands and Complexes.
> >Generating AM1-BCC charges.  This may be time consuming.
> >Ligand lig.1 has total charge 0
> >
> >Error from amberize_ligand; the name of the ligand is
> >    ASL
> >    Examine amberize_ligand.lig.1.out

> Test output file, showing /home/a-day/bin/amber/amber12/bin/divcon not
> found.  This is an AmberTools13 install.
> >a-day at a-has:~/bin/dock/dock6/install/test/amber_score_181l$ cat
> >amberize_ligand.lig.1.out
> >Using ligand file prefix: lig.1
> >Using antechamber options: -nc 0 -c bcc
> >Executing antechamber to generate the mol2 file with GAFF and charges.
> >
> >Total number of electrons: 100; net charge: 0
> >
> >Running: $AMBERHOME/bin/divcon
> >sh: 1: /home/a-day/bin/amber/amber12/bin/divcon: not found
> >Error: cannot run "$AMBERHOME/bin/divcon" of bcc() in charge.c properly,
> >exit
> >Running: /home/a-day/bin/dock/dock6/bin/bondtype -i
> >
> >Running: /home/a-day/bin/dock/dock6/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> >Executing parmchk to generate the force field parameters.
> >Cannot open file lig.1.gaff.mol2, exit
> >grep: lig.1.frcmod: No such file or directory
> >Executing LEaP to generate the Amber input files.
> >-I: Adding /home/a-day/bin/dock/dock6/parameters/leap/prep to search path.
> >Could not open file lig.1.frcmod: not found


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