Cannot generate .psf file

HADDOCK
1

I am trying to dock DNA over protein and is getting the following error. The error is psf files are not generating in the /begin directory.

AMBIG_TBL ./cro_air.tbl
PROJECT_DIR .
PDB_FILE2 ./DNA.pdb
looking for existing files
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/protein.psf…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/protein.pdb…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/DNA.psf…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/DNA.pdb…
waterdock false
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/protein.psf…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/protein.pdb…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/DNA.psf…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/DNA.pdb…
** waiting for the psf files…**
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/protein.psf…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/protein.pdb…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/DNA.psf…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/DNA.pdb…
** waiting for the psf files…**
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/protein.psf…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/protein.pdb…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/DNA.psf…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/DNA.pdb…
** waiting for the psf files…**
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/protein.psf…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/protein.pdb…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/DNA.psf…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/DNA.pdb…
** waiting for the psf files…**
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/protein.psf…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/protein.pdb…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/DNA.psf…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/DNA.pdb…
** waiting for the psf files…**
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/protein.psf…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/protein.pdb…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/DNA.psf…
waiting for /home/abwer/Downloads/haddock2.4-2022-01/examples/protein-dna/run1/begin/DNA.pdb…
Error in the topology generation: prot_psf_mol1 could not be created
=> HADDOCK stopped
##############################################################################
Finishing HADDOCK on: 2022-11-30 14:08:09
Au revoir.
Tot ziens.
Bye bye.

2

I checked the /begin/generate_1.out and getting the following error.

MESSage=NORM
** EVALUATE: symbol $OLD_MESSAGE set to “NORM” (string)**
** ECHO=TRUE {ON}**
** EVALUATE: symbol $OLD_ECHO set to TRUE (logical)**
** RTFRDR>set message=off echo=off end**
** %AUTOAN error encountered: exceeded MXRTT (RTF) parameter → recompile program**
** (CNS is in mode: SET ABORT=NORMal END)**

** ABORT mode will terminate program execution.**

** Program will stop immediately.**
** ============================================================**
** Maximum dynamic memory allocation: 8201488 bytes**
** Maximum dynamic memory overhead: 208 bytes**
** Program started at: 13:53:16 on 30-Nov-2022**
** Program stopped at: 13:53:16 on 30-Nov-2022**
** CPU time used: 0.0548 seconds**
** ============================================================**

3

Did you recompile CNS with the provided CNS code coming with haddock? Check the cns1.3 directory.

4

Thanks for the reply. How do you do that?
Best,
Gaurav

5

Hello Dr. Bonvin,

I figured it out. It was very clearly mentioned in the previous suggestions. Thanks for your help.

Best,
Gaurav