DOT 2.0 Frequently Asked Questions (FAQ)

Add a question to the FAQ list.


Sections

  1. Downloading & Installing DOT
  2. Preparing files for DOT using prepscript
  3. Platform specific problems

Downloading & Installing DOT

Question: I've followed the installation instructions in the manual, but when I try to run any program I get a "Cannot find <program>" error message.

Answer: Make sure the $DOT_ROOT environment variable is set up. $DOT_ROOT should be set to the top level directory containing the DOT installation. For example if you installed DOT in /usr/local/dot2.0 then $DOT_ROOT should be set to /usr/local/dot2.0. Also make sure you have correctly sourced, NOT executed, the setup.bash or setup.csh scripts.

If you are using the bash shell:

export DOT_ROOT=/usr/local/dot2.0
source $DOT_ROOT/bin/share/setup.bash

If you are using the csh shell:

setenv DOT_ROOT /usr/local/dot2.0
source $DOT_ROOT/bin/share/setup.csh

Preparing files for DOT using prepscript

Question: prepscript complains about the total molecular charge not being an integer. It worked in the tutorial but not when I made my own prepscript even when using the example .pdb files that came with DOT.

./prepscript 2>&1 |tee prepscript.log
 
Total molecular charge  +3.752
Total charge 3.7520 is not an integer (int_qt=4)
dot2-prep-mol-common quitting
dot2-prep-mol_common reported an error, prepscript quitting

Answer: A total charge off from an integral value by 0.248 (3.752 + 0.248 = 4.00) is almost always due to an unprotonated N-terminal amino acid!

Immediate Solution for Tutorial Example

When you build your own prepscript using gen-dot-prepscript, the line is:

dot2-prep-mol-common -p ugi.pdb -l $reslib -w moving
In the tutorial, the prepscript has had the flag -r Nterm3 added to the call to dot2-prep-mol-common:
dot2-prep-mol-common -r Nterm3 -p ugi.pdb -l $reslib -w moving
You need to edit your prepscript so that "-r Nterm3" is added to your dot2-prep-mol-common call.

Why?

ugi.pdb begins with residue number 3. The addition of -r Nterm3 to dot2-prep-mol-common passes information to the REDUCE program about the N-terminus of the peptide chain.

REDUCE, the program that adds hydrogen atoms to the PDB coordinates, automatically creates positively charged N-termini (builds 3 hydrogen atoms on the N atom) ONLY if the residue number is 1. Else it adds NO protons to the N atom. The Nterm[number] flag tells REDUCE to treat any N-terminal residue with a residue number up to and including [number] as a charged N-terminus. REDUCE will then add 3 hydrogen atoms to the N atom. An N-terminal residue is identified as any residue that has no preceding C=O group within a specified distance.

Note: If you create your own prepscript for the example coordinates, you will also need to add -r Nterm82 to the dot2-prep-mol-common call for the stationary molecule, udg.pdb, as it begins with residue 82.

dot2-prep-mol-common -r Nterm82 -p udg.pdb -l $reslib -w stationary

General procedure

For your own coordinates, you need to check the N-terminal residue numbers of your moving and stationary molecules. In addition, breaks in peptide chains also create N-termini. You must make sure the first residue after the break is properly protonated, or you will not have an integral charge.

Details for dealing with protonation of N-terminal residues are given in the Manual. Please see Chapter 4 "Prepscript -creating input files for DOT" under the Section "Protonation of N-terminal amino acids in proteins (currently section H.3a)"

Platform specific problems

Question: Is DOT available on Windows?

Answer: The DOT development team has not tested DOT on Windows, but the port should be possible. There are versions of all required packages on Windows under Cygwin, but the work of integration and testing has not been done and is not planned for the near future due to lack of resources. Users are welcome to try it on their own.