# Haddock examples in ./examples are failing on topology creation
**URL:** https://ask.bioexcel.eu/t/haddock-examples-in-examples-are-failing-on-topology-creation/3468
**Category:** HADDOCK
**Created:** [February 22, 2022, 2:38pm UTC](https://ask.bioexcel.eu/t/haddock-examples-in-examples-are-failing-on-topology-creation/3468 "2022-02-22T14:38:35Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@vassyli](https://ask.bioexcel.eu/u/vassyli)
#### Post date: [February 22, 2022, 2:38pm UTC](https://ask.bioexcel.eu/t/haddock-examples-in-examples-are-failing-on-topology-creation/3468/1 "2022-02-22T14:38:35Z")
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:
```auto
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?
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [February 24, 2022, 8:13am UTC](https://ask.bioexcel.eu/t/haddock-examples-in-examples-are-failing-on-topology-creation/3468/2 "2022-02-24T08:13:14Z")
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](http://protein-allhdg5-4.top) present in that dir?
What is the value of run\_dir in the run.cns file?
---
### Author:  [@vassyli](https://ask.bioexcel.eu/u/vassyli)
#### Post date: [February 24, 2022, 9:39am UTC](https://ask.bioexcel.eu/t/haddock-examples-in-examples-are-failing-on-topology-creation/3468/3 "2022-02-24T09:39:12Z")
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:
```auto
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:
````auto
#
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="./";`
---
### Author:  [@vassyli](https://ask.bioexcel.eu/u/vassyli)
#### Post date: [February 24, 2022, 11:30am UTC](https://ask.bioexcel.eu/t/haddock-examples-in-examples-are-failing-on-topology-creation/3468/4 "2022-02-24T11:30:54Z")
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.
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [February 24, 2022, 1:28pm UTC](https://ask.bioexcel.eu/t/haddock-examples-in-examples-are-failing-on-topology-creation/3468/5 "2022-02-24T13:28:38Z")
> 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.