Haddock examples in ./examples are failing on topology creation

HADDOCK
1

Dear all,

I’ve create a local installation of haddock and compiled CNS with the provided files (replaced them). Then, I’ve been trying to run the samples (no matter if it is HADDOCK-run-all-examples.csh or the individual scripts), but they all seem to abort on the topology creation step in CNS:

CNSsolve> 
 CNSsolve> if ($Toppar.prot_segid_$chain="") then 
 NEXTCD: condition evaluated as false
 CNSsolve>   evaluate($Toppar.prot_segid_$chain=encode($chain)) 
 CNSsolve> end if 
 CNSsolve> 
 CNSsolve> evaluate ($log_level=normal) 
 Assuming literal string "NORMAL"
 EVALUATE: symbol $LOG_LEVEL set to "NORMAL" (string)
 CNSsolve> 
 CNSsolve> topology 
 RTFRDR>   @@$topology_infile 
 %ASSFIL-ERR: error opening file .//toppar/protein-allhdg5-4.top
 %ASSFIL error encountered: Error accessing file
   (CNS is in mode: SET ABORT=NORMal END)
 *****************************************************
 ABORT mode will terminate program execution. 
 *****************************************************
 Program will stop immediately.
          ============================================================
           Maximum dynamic memory allocation:     8297488 bytes
           Maximum dynamic memory overhead:           960 bytes
           Program started at: 15:27:50 on 22-Feb-2022
           Program stopped at: 15:27:50 on 22-Feb-2022
           CPU time used:       0.0669 seconds
          ============================================================

What can I do?

2

Can you provide more details of your installation, like OS and where is haddock installed?

I assume the run1 dir is properly created if you get to that stage?
Is the toppar directory present in that dir?
Is the protein-allhdg5-4.top present in that dir?

What is the value of run_dir in the run.cns file?

3

Sure!

Haddock is running on a (virtualized) Ubuntu 20.04. Software is installed in ~/bin/cns_solve_1.3 and ~/bin/haddock2.4-2022-01. Python is 2.7.18, installed within an (active) anaconda environment. Haddock tools is installed to ~/bin/haddock2.4-2022-01/tools, paths have been adjusted in config.local for CNS:

set CNSTMP=/home/sauterb/bin/cns_solve_1.3/intel-x86_64bit-linux/bin/cns
set QUEUETMP=/bin/csh
set NUMJOB=1
set QUEUESUB=QueueSubmit_concat.py

haddock_configure.sh (and csh) point to the correct location of haddock tools.

Output of protein-protein/run-example.csh:

#
source ../../haddock_configure.csh
echo "=========================================================="
echo "=========================================================="
echo " RUNNING NOW E2A-HPR PROTEIN-PROTEIN DOCKING EXAMPLE"
echo "=========================================================="
echo "=========================================================="
haddock2.4 >&/dev/null
cd run1
patch -p0 -i ../run.cns.patch >&/dev/null
haddock2.4 >&haddock.out
cd ..
./ana_scripts/run_all.csh run1 >&/dev/null
../results-stats.csh run1
echo "=========================================================="
echo "=========================================================="
echo " E2A-HPR PROTEIN-PROTEIN DOCKING EXAMPLE COMPLETED"
echo "=========================================================="
echo "=========================================================="```

(but run1/begin/generate_1.out gives the error in the first post)

run1 directory is created, the toppar directory is empty. ../results-stats.csh gives this output:

```######################################################

  HADDOCK scoring water
______________________________________________________
=========== run1 =============

===> Cluster stats water <====

===> Cluster stats it1 <====

===> water single structure i-RMSD stats <====
no water first medium <2A - - - - - - -
no water first acceptable <4A - - - - - - -
no water best acceptable or higher - - - - - - -

===> it1 single structure i-RMSD stats <====
no it1 acceptable <2A - - - - - - -
no it1 first acceptable <4A - - - - - - -
no it1 best acceptable or higher - - - - - - -

===> it0 single structure i-RMSD stats <====
no it0 acceptable <2A - - - - - - -
no it0 first acceptable <4A - - - - - - -
no it0 best acceptable or higher - - - - - - -

===> Overall number of acceptable or better models <===
it0:   structures with i-RMSD<4A:  0
it0:   structures within best200 with i-RMSD<4A: 0
it0:   structures within best200 with i-RMSD<2A: 0
it0:   structures within best200 with i-RMSD<1A: 0
it1:   structures with i-RMSD<4A:  0
it1:   structures with i-RMSD<2A:  0
it1:   structures with i-RMSD<21:  0
water: structures with i-RMSD<4A:  0
water: structures with i-RMSD<2A:  0
water: structures with i-RMSD<1A:  0

Value of run_dir in examples/protein-protein/run1/run.cns is: {===>} run_dir="./";

4

Sorry for your time. It looks 7zip failed to completely unpack the toppar directory into the haddock folder - which is why nothing was copied and the run failed. After unpacking it again, the example seems to run so far.

5

PS - The run reports ./tools/check-error-message.csh to be missing. Its not contained in haddock tools.

Well it is in the distribution package.