# Cannot generate .psf file

**URL:** <https://ask.bioexcel.eu/t/cannot-generate-psf-file/4016>\
**Category:** HADDOCK\
**Created:** [November 30, 2022, 7:27pm UTC](https://ask.bioexcel.eu/t/cannot-generate-psf-file/4016 "2022-11-30T19:27:42Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![gaurav.sharmapsit](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/gaurav.sharmapsit/32/689_2.png) [@gaurav.sharmapsit](https://ask.bioexcel.eu/u/gaurav.sharmapsit)\
**Post date:** [November 30, 2022, 7:27pm UTC](https://ask.bioexcel.eu/t/cannot-generate-psf-file/4016/1 "2022-11-30T19:27:42Z")

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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.**

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<div class="post-metadata">

**Author:** ![gaurav.sharmapsit](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/gaurav.sharmapsit/32/689_2.png) [@gaurav.sharmapsit](https://ask.bioexcel.eu/u/gaurav.sharmapsit)\
**Post date:** [November 30, 2022, 7:28pm UTC](https://ask.bioexcel.eu/t/cannot-generate-psf-file/4016/2 "2022-11-30T19:28:51Z")

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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\*\*  
\*\* ============================================================\*\*

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<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [November 30, 2022, 8:02pm UTC](https://ask.bioexcel.eu/t/cannot-generate-psf-file/4016/3 "2022-11-30T20:02:56Z")

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

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<div class="post-metadata">

**Author:** ![gaurav.sharmapsit](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/gaurav.sharmapsit/32/689_2.png) [@gaurav.sharmapsit](https://ask.bioexcel.eu/u/gaurav.sharmapsit)\
**Post date:** [November 30, 2022, 8:20pm UTC](https://ask.bioexcel.eu/t/cannot-generate-psf-file/4016/4 "2022-11-30T20:20:14Z")

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

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<div class="post-metadata">

**Author:** ![gaurav.sharmapsit](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/gaurav.sharmapsit/32/689_2.png) [@gaurav.sharmapsit](https://ask.bioexcel.eu/u/gaurav.sharmapsit)\
**Post date:** [November 30, 2022, 9:00pm UTC](https://ask.bioexcel.eu/t/cannot-generate-psf-file/4016/5 "2022-11-30T21:00:51Z")

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Hello Dr. Bonvin,

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

Best,  
Gaurav