# Error: module name and a source file **URL:** \ **Category:** HADDOCK\ **Created:** [December 12, 2017, 9:59am UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674 "2017-12-12T09:59:42Z")\ **Posts on this page:** 17\ **Page:** 1
**Author:** ![garima.tanwar](https://avatars.discourse-cdn.com/v4/letter/g/43a26b/32.png) [@garima.tanwar](https://ask.bioexcel.eu/u/garima.tanwar)\ **Post date:** [December 12, 2017, 9:59am UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/1 "2017-12-12T09:59:42Z")
In the need of Start HADDOCK in the directory where we saved the new.html file by typing `haddock2.2` shows in terminal: `haddock2.2: command not found` after typing: `haddock 2.2` shows in terminal: `target ‘2.2’ is not a module name or a source file` ---
**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:** [December 12, 2017, 1:15pm UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/2 "2017-12-12T13:15:29Z")
Refer to: [http://www.bonvinlab.org/software/haddock2.2/manual/](http://www.bonvinlab.org/software/haddock2.2/manual/) and: [http://www.bonvinlab.org/software/haddock2.2/tut\_e2a-hpr-csp/](http://www.bonvinlab.org/software/haddock2.2/tut_e2a-hpr-csp/) ---
**Author:** ![garima.tanwar](https://avatars.discourse-cdn.com/v4/letter/g/43a26b/32.png) [@garima.tanwar](https://ask.bioexcel.eu/u/garima.tanwar)\ **Post date:** [December 13, 2017, 7:16am UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/3 "2017-12-13T07:16:58Z")
Thanks a lot sir for replying… Actually this error was resolved by entering into haddock 2.2 directory and copy new.html file in that and typing: ` tcsh` entered into c-shell and type: `source haddock_configure.csh` `haddock2.2` then its running run1 directory has been created in which we have to edit run.cns file But it gives error: waterdock false Help me to resolve this!! ![waterdock_error](https://dub1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/8a471eee4b31e858b97840f1fa2df11162831636.png) ---
**Author:** ![garima.tanwar](https://avatars.discourse-cdn.com/v4/letter/g/43a26b/32.png) [@garima.tanwar](https://ask.bioexcel.eu/u/garima.tanwar)\ **Post date:** [December 13, 2017, 9:58am UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/4 "2017-12-13T09:58:57Z")
Now showing: ``` ln: failed to create symbolic link 'protocols/cns1': File exists waterdock false waiting for the psf files... ``` ---
**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:** [December 13, 2017, 11:25am UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/5 "2017-12-13T11:25:52Z")
Did you install CNS? Did you define its location correctly in run.cns? ---
**Author:** ![garima.tanwar](https://avatars.discourse-cdn.com/v4/letter/g/43a26b/32.png) [@garima.tanwar](https://ask.bioexcel.eu/u/garima.tanwar)\ **Post date:** [December 13, 2017, 11:40am UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/6 "2017-12-13T11:40:23Z")
Yes, but I don’t have ifort installed. ---
**Author:** ![garima.tanwar](https://avatars.discourse-cdn.com/v4/letter/g/43a26b/32.png) [@garima.tanwar](https://ask.bioexcel.eu/u/garima.tanwar)\ **Post date:** [December 13, 2017, 12:00pm UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/7 "2017-12-13T12:00:48Z")
Now showing this error ![waterdock_error1](https://dub1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/ae4ee479b9abab268538c1521a9da7eb20ac5235.png) ---
**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:** [December 13, 2017, 12:32pm UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/8 "2017-12-13T12:32:18Z")
No CNS = no docking! Consider using our web server instead if you can not compile CNS… ---
**Author:** ![garima.tanwar](https://avatars.discourse-cdn.com/v4/letter/g/43a26b/32.png) [@garima.tanwar](https://ask.bioexcel.eu/u/garima.tanwar)\ **Post date:** [December 13, 2017, 2:01pm UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/9 "2017-12-13T14:01:51Z")
yup…its compiled and docking runs… But this error occurs: `Error in the topology generation: prot_psf_A could not be created` ---
**Author:** ![joaor](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/joaor/32/194_2.png) [@joaor](https://ask.bioexcel.eu/u/joaor)\ **Post date:** [December 13, 2017, 2:15pm UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/10 "2017-12-13T14:15:49Z")
Something is wrong with your CNS installation. HADDOCK tries to launch the calculations and they fail. Have a look at the `.out` files in the `begin/` directory of your run. What is the error message? As @amjjbonvin said, maybe you should try using the web server, unless you are doing something really out of the ordinary. ---
**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:** [December 13, 2017, 2:17pm UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/11 "2017-12-13T14:17:28Z")
Make sure to define the correct path in run.cns Make sure that CNS is working Start a fresh run (or remove protocols/cns1 and all \*.out files in the begin dir) ---
**Author:** ![garima.tanwar](https://avatars.discourse-cdn.com/v4/letter/g/43a26b/32.png) [@garima.tanwar](https://ask.bioexcel.eu/u/garima.tanwar)\ **Post date:** [December 14, 2017, 12:52pm UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/12 "2017-12-14T12:52:44Z")
First of all thanks for your concern. Let me show you the `generated A.out` file in the `/begin` directory %SETFPEPS increase value of MXFPEPS2 and recompile %SETFPEPS error encountered: Could not determine machine epsilon (CNS is in mode: SET ABORT=NORMal END) \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\* ABORT mode will terminate program execution. \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\* Program will stop immediately. ============================================================ Maximum dynamic memory allocation: 0 bytes Maximum dynamic memory overhead: 0 bytes Program started at: \00\00\00\00\00\00\00\00 on \00\00\00\00\00\00\00\00\00\00\00 Program stopped at: 06:01:31 on 15-Dec-2017 CPU time used: 0.0040 seconds ============================================================ ---
**Author:** ![garima.tanwar](https://avatars.discourse-cdn.com/v4/letter/g/43a26b/32.png) [@garima.tanwar](https://ask.bioexcel.eu/u/garima.tanwar)\ **Post date:** [December 14, 2017, 1:02pm UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/13 "2017-12-14T13:02:35Z")
Dear sir, I surely define the correct path in run.cns But I am not pretty sure about the working of CNS… As `.out` files were generated in the `begin` directory, I think its working. ---
**Author:** ![joaor](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/joaor/32/194_2.png) [@joaor](https://ask.bioexcel.eu/u/joaor)\ **Post date:** [December 14, 2017, 1:27pm UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/14 "2017-12-14T13:27:03Z")
There you go. You need to look for the `MSFPEPS2` variable in the CNS source code (grep the name on all `.f` files) and increase its value. Then you must recompile CNS. Again, unless you are doing something _extremely_ unique, use the webserver. It’s free and it just works. ---
**Author:** ![garima.tanwar](https://avatars.discourse-cdn.com/v4/letter/g/43a26b/32.png) [@garima.tanwar](https://ask.bioexcel.eu/u/garima.tanwar)\ **Post date:** [December 15, 2017, 4:49am UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/15 "2017-12-15T04:49:49Z")
Sorry, but I am not getting your point… please explain step by step… I am trying `$grep MSFPEPS2 xyz.f` xyz-\>all .f files n source directory of CNSsolve And also let me clear you why I am stuck with the software, because I want these results for further research and webserver’s results will be lost after 7 days and I was also tried web server, it’s too showing error ``` Error message Status: Out of sync (in children) Invalid members: ['p2'] Member p2 (Second molecule) : Out of sync (in children) Invalid members: ['r'] Member r (Restraint definition) : Out of sync (invalid) Exception: HaddockValidationError: You manually defined passive residues, but also that they should be determined automatically ``` ---
**Author:** ![mtrellet](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/mtrellet/32/42_2.png) [@mtrellet](https://ask.bioexcel.eu/u/mtrellet)\ **Post date:** [December 15, 2017, 7:56am UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/16 "2017-12-15T07:56:19Z")
Hello, Despite the web servers results deleted after 7 days, the ensemble of the results, together with the summary page and the analysis that are done ONLY on the web server can be downloaded as a tar archive upon success of your run. The error you report with the web server is, as it is stated, due to the fact that you input residue IDs in the passive field of the form for the 2nd molecule but you did not uncheck the option “Define passive residues automatically around the active residues” just below the list input. Try again with that and this should go true of no other error are present. ---
**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:** [December 15, 2017, 8:05am UTC](https://ask.bioexcel.eu/t/error-module-name-and-a-source-file/674/17 "2017-12-15T08:05:12Z")
Really try first the server. Once you have a successful run (you are doing something wrong - not the server). `HaddockValidationError: You manually defined passive residues, but also that they should be determined automatically` Correct that error and try again. You can download all results and save them as long as you wish for on your computer. Further: 1. Did you check your CNS installation. Can you start CNS manually? FFT3C: Using FFTPACK4.1 CNSsolve\> ```auto One this is working, you can then try running first one of the provided examples. A protocol for running a local version of HADDOCK can be found in: J.P.G.L.M Rodrigues, E. Karaca and A.M.J.J. Bonvin. Information-driven structural modelling of protein-protein interactions. Methods in Molecular Biology: Molecular Modelling of Proteins. Ed. Andreas Kokul. Humana Press Inc. 399-424 (2015). http://link.springer.com/protocol/10.1007/978-1-4939-1465-4_18 And this forum is searchable - try first to look for answers. There are multiple threads about CNS problems, e.g. http://ask.bioexcel.eu/t/cns-errors-before-after-recompilation/54 ```