DOCK:FAQ

This is the DOCK FAQ. It covers all versions of DOCK. There are other FAQs available at this site.

All DOCK versions

Q0.2. What is the current version of DOCK?

DOCK 6.1 was released in December 2006.

Q0.3. What about accessory programs?

Where do I get DMS? DMS is freely available from the UCSF Computer Graphics Lab.

Q0.4. Tools to protonate the receptor?

We use Sybyl. You can also use REDUCE.

One user suggested using VEGA ZZ [1]

DOCK 6 Specific

Q6.1 I get an error with mmolex when compiling DOCK6?

When I compile DOCK, I get something like the following error:

g++ -O2 -o dock6 amber_typer.o base_mpi.o base_score.o conf_gen.o dock.o dockmol.o library_file.o master_score.o orient.o score.o simplex.o utils.o score_solvent.o score_amber.o sasa.o score_chemgrid.o nab/nab.a -lm -lpthread ld: Undefined symbols: _mmolex make: *** [dock6] Error 1

What is causing the error and how do I fix it?

Answer

DOCK 6 requires a lexical analyzer generator; example Unix command names are lex and flex. All classical Unices have lex. Linuces usually have flex. But this undefined symbol is caused by a missing lexical analyzer generator. (It may be that some users are not installing enough of their Linux.) In particular, dock6/src/dock/nab/lex.mm_options.c either will not exist or will have a size of zero if a lexical analyzer generator is missing.

Here are some suggestions:

• Verify that dock6/src/dock/nab/lex.mm_options.c is broken or missing.
• Look for a lexical analyzer generator on your machine.
• Verify the definition of the macro LEX in the configuration file, dock6/install/config.h; LEX should be assigned the name of your lexical analyzer generator.
• Install a lexical analyzer generator if one is not found. flex: The Fast Lexical Analyzer is free software.
• Try our dock6/src/dock/nab/lex.mm_options.c:
• Change directory to dock6/src/dock/nab and execute make clean. Download lex.mm_options.c. (This file was generated by flex version 2.5.4 on Red Hat Enterprise Linux AS release 3 (Taroon Update 6).) Copy it to dock6/src/dock/nab/lex.mm_options.c. Edit dock6/install/config.h and make the LEX definition equal to flex, i.e LEX= flex. Restart the installation: cd install; make install

Q6.2 I get an error in /usr/include/mpi++.h:1473

FAQ:MPICH2

• When running DOCK with amber_score, I get can't open file lig.1.amber.pdb FAQ:AMBERHOME

DOCK 5 Specific

Note: we recommend upgrading from DOCK5.x to DOCK 6. There is really no good reason to still be using DOCK 5. Many of the problems in DOCK 5 are fixed in DOCK 6.

DOCK 4 Specific

Note: DOCK 4.0.2 is an old program, but still in use by some people for some purposes.

DOCK 3.5.54 Specific

Note: DOCK 3.5.54 is the version used by DOCK Blaster. However, if you are using DOCK 3.5.54 via DOCK Blaster, we encourage you to use the FAQ for the interface DOCK Blaster:FAQ