This program aims to search for a water molecule's energy positions in cavities of proteins having minimum energy. For more information, please refer to the original Zhang and Hermans paper.
Dowser's official link is (was?) http://danger.med.unc.edu/hermans/dowser/dowser.htm. However, it is hardly ever available, which is why I decided to upload the Dowser code to ensure program availability.
Prior to installing Dowser, update the system package index. For example, on Debian based distributions, type:
sudo apt update
sudo apt install build-essential
You need a FORTRAN (e.g. gfortran, ifort) and C (e.g. gcc) compilers in Linux to install Dowser. These can be installed on Debian based distributions with:
sudo apt-get install gfortran gcc
On this repository, the make configuration in file CODE/Makearch.linux already includes gfortran as the FORTRAN compiler. If you are using another compiler, or in case you are using any other of the available architectures, please modify the line F77 = f77 inside the corresponding make configuration file to meet your specific situation.
Also, this code was written back in the day using the K&R C (pre-ANSI) standard. An attempt to compile it with a modern C standard results in compilation errors due to old-style function definitions. To ignore them, you need to include the flags -Wno-old-style-definition -std=gnu89 into the ARCH_COPTS list of your architecture make file.
If you are using the Linux architecture, this has already been done for you (see CODE/Makearch.linux), otherwise, include them by yourself into the equivalent CODE/Makearch.[your-architecture] before attempting to compile the Dowser source code.
Once you have downloaded the code, get into its directory, and grant the following scripts with execution rights if they don't already have it. Then execute the installation:
chmod u+x Install bin/dowser bin/append_dowser_water bin/append_index bin/cleanup_dowser bin/dryer bin/ms2pdb
./Install
As a result, you should obtain a series of new executable under directory bin/linux/ (or any other architecture you had selected). Make sure to grant them execution rights too:
chmod u+x bin/linux/*
Now, to make these executable accessible from anywhere on the system, export the Dowser program location to your PATH. For BASH, edit your .bashrc or .bash_profile file by adding:
export DOWSER=/path/to/dowser # write your Dowser absolute installation path here
export DOW_MACH=linux
export PATH=$PATH:$DOWSER/bin:$DOWSER/bin/$DOW_MACH
For CSH type:
setenv DOWSER /path/to/dowser # write the Dowser absolute installation path here
setenv DOW_MACH linux
set path = ( $path $DOWSER/bin $DOWSER/bin/$DOW_MACH )
And finally, source the edited file (whichever is your case) to make the changes take effect:
source .bashrc
or
source .bash_profile
To meet pyARMm requirements, new residues have been added to file DATA/atomdict.db. Furthermore, it needs to be pointed out that residue HIS TERM NH3 COO has been modified from
RESIDUE HIS TERM NH3 COO
ATOM HIS N C CA 1.320 114.0 180.0 -0.280 N
ATOM HIS H N NOT 1.000 123.0 0.0 0.280 H
ATOM HIS CA N C 1.470 123.0 180.0 0.000 CH1
ATOM HIS CB CA CG 1.530 110.0 60.0 0.000 CH2
ATOM HIS CG CB ND1 1.530 112.0 180.0 0.000 CR
ATOM HIS CD2 CG NOT 1.360 132.0 180.0 0.000 CHR
ATOM HIS ND1 CG CE1 1.390 122.0 0.0 0.128 N
ATOM HIS HD1 ND1 NOT 1.000 126.0 0.0 0.192 H
ATOM HIS CE1 ND1 NE2 1.320 108.0 180.0 0.259 CHR
ATOM HIS NE2 CE1 NOT 1.310 109.0 0.0 -0.579 N
ATOM HIS C CA N 1.530 110.0 180.0 0.380 CR
ATOM HIS O C NOT 1.240 121.0 0.0 -0.380 O
to
RESIDUE HIS TERM NH3 COO
ATOM HIS N C CA 1.320 114.0 180.0 -0.3479 N
ATOM HIS H N NOT 1.000 123.0 0.0 0.2747 H
ATOM HIS CA N C 1.470 123.0 180.0 -0.1354 CH1
ATOM HIS CB CA CG 1.530 110.0 60.0 -0.0414 CH2
ATOM HIS CG CB ND1 1.530 112.0 180.0 -0.0012 CR
ATOM HIS CD2 CG NOT 1.360 132.0 180.0 -0.1141 CHR
ATOM HIS ND1 CG CE1 1.390 122.0 0.0 -0.1531 N
ATOM HIS HD1 ND1 NOT 1.000 126.0 0.0 0.2317 H
ATOM HIS CE1 ND1 NE2 1.320 108.0 180.0 -0.0170 CHR
ATOM HIS NE2 CE1 NOT 1.310 109.0 0.0 -0.1718 N
ATOM HIS HE2 NE2 NOT 1.000 126.0 180.0 0.2681 H
ATOM HIS C CA N 1.530 110.0 180.0 0.7341 CR
ATOM HIS O C NOT 1.240 121.0 0.0 -0.5894 O