Issue in installing Haddock2.2?

HADDOCK
1

Dear Friends,

I am using haddock for the first time, and trying to install it in ubuntu 18.04. I went through the installation tutorial; however, I am facing issue in getting “NACCESS” software, and facing difficulty in using “PALES” and "“TENSOR” software. When I run
./pales; it gives me .“bash: ./pales: No such file or directory”

and, for tensor, I get the same error.

Could you please let me know how can I get these softwares. My machine is x86_64. Thank you for your time!

2

No need for pales and tensor

And if needed you might replace naccess by freesasa.

3

Thanks does this mean to run haddock., I can:

a) replace naccess with freesasa executable?

b) remove the path to pales and tensor from this configuration file:

#!/bin/bash

HADDOCK configuration file

HADDOCK=“/media/Deepak/NPRP10/softwares/haddock/haddock2.2”
HADDOCKTOOLS=“$HADDOCK/tools”
PYTHONPATH=“${PYTHONPATH}:$HADDOCK”
alias haddock2.2=which python $HADDOCK/Haddock/RunHaddock.py

Define location of third party software

NACCESS=“/home/software/software/bin/naccess”
PALES=“/home/software/software/bin/pales”
PROFIT=“/home/software/software/bin/profit”
TENSOR2=“/home/software/software/bin/tensor2”

export HADDOCK HADDOCKTOOLS PYTHONPATH NACCESS PALES PROFIT TENSOR2

4

naccess is only used in setting up runs. It is not directly used by HADDOCK when running

5

thanks! I get that point, but my question is;.

What changes I need to make in the haddock configuration file in my previous message?

a) can I replace the naccess path with freesasa executable path?

b) Can I remove the paths to tensor and pales?

So the new configuration file looks like this?

#!/bin/bash

HADDOCK configuration file

HADDOCK=“/media/Deepak/NPRP10/softwares/haddock/haddock2.2”
HADDOCKTOOLS=“$HADDOCK/tools”
PYTHONPATH=“${PYTHONPATH}:$HADDOCK”
alias haddock2.2= which python $HADDOCK/Haddock/RunHaddock.py

Define location of third party software

FREESASA=“/home/software/software/bin/freesasa”
PROFIT=“/home/software/software/bin/profit”

export HADDOCK HADDOCKTOOLS PYTHONPATH FREESASA PROFIT

Thanks!

6

You can remove all paths (or comment them out) to pales, tensor and naccess.

Of course if you intend to use NMR RDC restraints, you might want pales for manual post-analysis.

And naccess or freesasa can be used to identify solvent-accessible residues, e.g. as described in:

http://www.bonvinlab.org/software/haddock2.2/generate_air_help/#CSP
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