Bin error when try to execute the source ./haddock.config

You can still use haddock…

Comment out the other lines

But again haddock is perfectly fine even if you get those messages. This command only defines some environment variable and path and does not start haddock

I just removed all those lines but when I try to execute source ./haddock_configure.sh it did not give any output/did not open the program as well

Which is normal… Did you read the tutorial???

I have go through the tutorial and I followed all the steps in the installation instructions as well.
I did not get any error massage while installing but still I am unable to launch the software

Follow the entire tutorial describing all the steps to setup and launch a run…

There is no graphical interface.

I have followed the instructions as given. I have copied the example files and the .param files to the directory where I have all my input structure but when I typed haddock2.4 it gives back me with a error
bash: haddock2.4: command not found…

Which means your configuration is either wrong, or you did not source first the haddock_configure.sh script

That is what my actual and first query is.
when I try source haddock_configure.sh
it gives me the follwing error
source haddock_configure.sh
/usr/bin/which: no naccess in (/data/apps/gromacs-2019.1/bin:/data/apps/cmake-3.14.3/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/opt/BiO/gridengine/bin:/opt/BiO/gridengine/bin/lx-amd64:/home/kmpr/softwares/pymol/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/data/apps/gromacs-2019.1/bin:/data/apps/cmake-3.14.3/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/opt/BiO/gridengine/bin:/opt/BiO/gridengine/bin/lx-amd64:/home/kmpr/softwares/pymol/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/data/apps/gromacs-2019.1/bin:/data/apps/cmake-3.14.3/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/opt/BiO/gridengine/bin:/opt/BiO/gridengine/bin/lx-amd64:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/kmpr/.local/bin:/home/kmpr/bin:/root/software/bin:/root/software/bin:/root/software/haddock-tools:/root/software/freesasa-2.0.3/src)
/usr/bin/which: no pales in (/data/apps/gromacs-2019.1/bin:/data/apps/cmake-3.14.3/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/opt/BiO/gridengine/bin:/opt/BiO/gridengine/bin/lx-amd64:/home/kmpr/softwares/pymol/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/data/apps/gromacs-2019.1/bin:/data/apps/cmake-3.14.3/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/opt/BiO/gridengine/bin:/opt/BiO/gridengine/bin/lx-amd64:/home/kmpr/softwares/pymol/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/data/apps/gromacs-2019.1/bin:/data/apps/cmake-3.14.3/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/opt/BiO/gridengine/bin:/opt/BiO/gridengine/bin/lx-amd64:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/kmpr/.local/bin:/home/kmpr/bin:/root/software/bin:/root/software/bin:/root/software/haddock-tools:/root/software/freesasa-2.0.3/src)
/usr/bin/which: no profit in (/data/apps/gromacs-2019.1/bin:/data/apps/cmake-3.14.3/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/opt/BiO/gridengine/bin:/opt/BiO/gridengine/bin/lx-amd64:/home/kmpr/softwares/pymol/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/data/apps/gromacs-2019.1/bin:/data/apps/cmake-3.14.3/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/opt/BiO/gridengine/bin:/opt/BiO/gridengine/bin/lx-amd64:/home/kmpr/softwares/pymol/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/data/apps/gromacs-2019.1/bin:/data/apps/cmake-3.14.3/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/opt/BiO/gridengine/bin:/opt/BiO/gridengine/bin/lx-amd64:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/kmpr/.local/bin:/home/kmpr/bin:/root/software/bin:/root/software/bin:/root/software/haddock-tools:/root/software/freesasa-2.0.3/src)
/usr/bin/which: no tensor2 in (/data/apps/gromacs-2019.1/bin:/data/apps/cmake-3.14.3/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/opt/BiO/gridengine/bin:/opt/BiO/gridengine/bin/lx-amd64:/home/kmpr/softwares/pymol/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/data/apps/gromacs-2019.1/bin:/data/apps/cmake-3.14.3/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/opt/BiO/gridengine/bin:/opt/BiO/gridengine/bin/lx-amd64:/home/kmpr/softwares/pymol/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/data/apps/gromacs-2019.1/bin:/data/apps/cmake-3.14.3/bin:/data/apps/openmpi-4.0.0/bin:/usr/local/cuda-10.1/bin:/opt/BiO/gridengine/bin:/opt/BiO/gridengine/bin/lx-amd64:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/kmpr/.local/bin:/home/kmpr/bin:/root/software/bin:/root/software/bin:/root/software/haddock-tools:/root/software/freesasa-2.0.3/src)

And when I removed the lines from config.sh file it gives me this.
https://ask.bioexcel.eu/t/bin-error-when-try-to-execute-the-source-haddock-config/3156/4?u=wmunees47

But you told me that, this is not an issue for running the haddock and finally I end up with this

What is the current content of your haddock_configure.sh file?

Again, most users don’t have those issues…
Did you follow step-by-step all installation instructions?

#!/bin/bash

HADDOCK configuration file

HADDOCK="/root/software/haddock2.4-2021-05"
HADDOCKTOOLS="$HADDOCK/tools"
PYTHONPATH="${PYTHONPATH}:$HADDOCK"
alias haddock2.4="$(which python) $HADDOCK/Haddock/RunHaddock.py"
#alias haddock2.4="/home/enmr/software/python/bin/python $HADDOCK/Haddock/RunHaddock.py"

Define location of third party software

NACCESS=which naccess
PALES=which pales
PROFIT=which profit
TENSOR2=which tensor2

export HADDOCK HADDOCKTOOLS PYTHONPATH NACCESS PALES PROFIT TENSOR2

And the content of my conf.local file is

set CNSTMP=/root/software/cns_solve_1.3/intel-x86_64bit-linux/source/cns_solve-2107101242.exe
set QUEUETMP=/bin/csh
set NUMJOB=32
set QUEUESUB=QueueSubmit_concat.py

Looks correct to me.

You should however make sure that you are using python2.7 with haddock.

Also after you have sourced the haddock-configure.sh script, check if the haddock2.4 alias is properly defined. It should.

Type alias to check all defined aliases

alias
alias cp=‘cp -i’
alias egrep=‘egrep --color=auto’
alias fgrep=‘fgrep --color=auto’
alias grep=‘grep --color=auto’
alias l.=‘ls -d .* --color=auto’
alias licstart=’$SCHRODINGER/licadmin start’
alias licstat=’$SCHRODINGER/licadmin stat’
alias ll=‘ls -l --color=auto’
alias ls=‘ls --color=auto’
alias maestro=’$SCHRODINGER/maestro’
alias mv=‘mv -i’
alias pycharm=’/data/apps/pycharm-community-2019.3.3/bin/pycharm.sh’
alias rm=‘rm -i’
alias which=‘alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde’

please tell me how to give input to haddock in bashrc?

And this is after sourcing the haddock_configure.sh script in the same terminal window???

Yes it is after sourcing the haddock_configure.sh

Can’t be… a haddock2.4 alias should have been defined…

Try typing all commands defined in haddock_configure.sh manually in the terminal window.

Make sure that the which python command is working and pointing to a python2.7 installation. If not define the exact path to python2.7

when I try to execute which python it gives me /usr/bin/python
and which python2.7 gives me /usr/bin/python2.7

I try to execute all the commands from terminal but it doesnt included in bashrc file.

Next I try to insert those files in bashrc file itself

The commands I included in bashrc is
################HADDOCK######
export HADDOCK=/root/software/haddock2.4-2021-05
export HADDOCKTOOLS=$HADDOCK/tools
export PYTHONPATH="/usr/bin/python2.7
alias haddock2.4="$(which python2.7) $HADDOCK/Haddock/RunHaddock.py
##############################
But it gives me
bash: alias: python2.7: not found
bash: alias: :/root/software/haddock2.4-2021-05: not found

Please help me sortout this issue

For your kind information the contents of my haddock_conf.sh is here

I would suggest to try first to get it running simply from the command line.
No need to include it in your bashrc file.

At this time it is more a Linux support issue rather than haddock issue.

It might be more efficient if you can find some experienced local user to help you.

Also under which operating system are you doing all this?

As I mentioned here I have tried with terminal it does’t work so then only i went to bashrc
And I am using centos 7

Sorry - but we can’t help more at this stage. Please find some local Linux expert to help you.

May-be one last thing to try is to run it under csh instead of bash, sourcing instead the haddock_configure.csh script.

But if executing the commands one by one in a terminal window does not work, then something is wrong with your system or there are typos.