Dear All
@amjjbonvin
Hello
I am running haddock2.4 from local installation and the installation process was pretty smooth.
However, I ran into an error while running run.cns which points to another file (./protocols/initialize.cns) that seems to exist.
I am unable to resolve it.
Here is the error message:
CNSsolve>
CNSsolve>@RUN:protocols/initialize.cns(iteration=$iteration;)
%XXNXTFI-ERR: invalid or unknown path-name: “RUN”:
@RUN:protocols/initialize.cns(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
%ASSFIL-ERR: error opening file RUN:protocols/initialize.cns
%ASSFIL error encountered: Error accessing file
(CNS is in mode: SET ABORT=NORMal END)
ABORT mode will terminate program execution.
Program will stop immediately.
Did you follow our online tutorial for the local installation?
https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-local-tutorial/
Are you able to run any of the examples or tests?
Thanks for the prompt reply.
The local installation was successful and as mentioned in the tutorial.
I am unable to run the examples as well, the same error pops up.
Then something is wrong with your setup…
It can’t be successful if you can’t run the examples or tests.
Are you sourcing the haddock_configure.csh/sh script first?
Describe exactly all steps you are doing until this error message pops up (i.e. exact commands you are giving)
Hello @amjjbonvin
Then something is wrong with your setup…
It can’t be successful if you can’t run the examples or tests.
You are right. This is something I noticed when I reinstalled haddock2.4. I perhaps missed to see this the first time.
This is how is tried installing after I compiled cns3.1
./install.csh config.local
Setting up QueueSubmit to QueueSubmit_concat.py
fatal: not a git repository (or any of the parent directories): .git >>>>>> perhaps something not right?
fatal: not a git repository (or any of the parent directories): .git >>>>>> perhaps something not right?
Now compiling HADDOCK utilities
cd tools;make
make[1]: Entering directory ‘/opt/haddock2.4/tools’
make cluster_struc contact contact-chainID haddock-decompress-fastfunc contact_fcc contact_fcc_lig
make[2]: Entering directory ‘/opt/haddock2.4/tools’
make[2]: ‘cluster_struc’ is up to date.
make[2]: ‘contact’ is up to date.
make[2]: ‘contact-chainID’ is up to date.
make[2]: ‘haddock-decompress-fastfunc’ is up to date.
make[2]: ‘contact_fcc’ is up to date.
make[2]: ‘contact_fcc_lig’ is up to date.
make[2]: Leaving directory ‘/opt/haddock2.4/tools’
make[1]: Leaving directory ‘/opt/haddock2.4/tools’
HADDOCK2.4 configured
to use it source first haddock_configure.csh/sh
Are you sourcing the haddock_configure.csh/sh script first?
Yes, before every run I would source haddock_configure.csh.
Describe exactly all steps you are doing until this error message pops up (i.e. exact commands you are giving)
step 1> Cleaning all the pdb files as mentioned in the basic tutorial for protein-protein docking.
a) Remove chain ID and SEQ ID: pdb_chain | pdb_seg ><PDB_clean>
b) validate: pdb_validate
c) Find gaps: pdb_gap
d) define restrains between chains in case of more than 1 units: restrain_bodies.py
>unambig.tbl
c) Filter passive residues by SASA using freesasa: freesasa --format=rsa >.rsa
Step 2> Generate restaints files from active and passive residues: active-passive-to-ambig.py rec-act-
pass.txt lig-act-pass.txt >rec-lig-ambig.tbl
Step3> prepare the run.param file. The contents are as follows:
AMBIG_TBL=rec-lig-ambig.tbl
HADDOCK_DIR=/opt/haddock2.4
N_COMP=2
PDB_FILE1=rec.pdb
PDB_FILE2=lig.pdb
PROJECT_DIR=./
PROT_SEGID_1=A
PROT_SEGID_2=B
RUN_NUMBER=1
UNAMBIG_TBL=unambig.tbl
Step4> source haddock_configure.csh and then run the haddock2.4 command. It runs without any errors and creates a “run1” directory.
Step 5> run the haddock2.4 command in the run1 directory. And this is the step I am getting the error.
Thanks Once again
Hello @amjjbonvin
The problem was the faulty installation of cns. And once I reinstall compiled it, there was no problem. The examples are running running file.
Thank you!!
Perfect - problem solved! :-))
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