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?

FAQ:mmolex

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