# Error when running $WDIR/encode-contacts.csh structures/it0/Acontacts.lis AcrB\_contacts.pdb **URL:** \ **Category:** HADDOCK\ **Created:** [November 26, 2017, 4:07am UTC](https://ask.bioexcel.eu/t/error-when-running-wdir-encode-contacts-csh-structures-it0-acontacts-lis-acrb-contacts-pdb/640 "2017-11-26T04:07:20Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![shawnteh1711](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@shawnteh1711](https://ask.bioexcel.eu/u/shawnteh1711)\ **Post date:** [November 26, 2017, 4:07am UTC](https://ask.bioexcel.eu/t/error-when-running-wdir-encode-contacts-csh-structures-it0-acontacts-lis-acrb-contacts-pdb/640/1 "2017-11-26T04:07:20Z")
I already create the AcrB\_contacts.pdb according to small molecule binding site tutorial using cygwin under tcsh shell, and when i trying to encode contacts into the b-factor column of PDB file using the following command: $WDIR/encode-contacts.csh structures/it0/Acontacts.lis AcrB\_contacts.pdb i encounter the following error: /ana\_script/zone\_b command not found. ![image](https://dub1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/77299876349ffa0ad3a827846f5c4fbde1e7fd33.png) However, when i checked the program zone\_b F file is in the ana\_scripts directory. Would appreciate if anyone could reply and explain to me how to solve this. Thank you. ---
**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 26, 2017, 4:16pm UTC](https://ask.bioexcel.eu/t/error-when-running-wdir-encode-contacts-csh-structures-it0-acontacts-lis-acrb-contacts-pdb/640/2 "2017-11-26T16:16:01Z")
Try to compile zone\_b.f in the ana\_script directory. We are only providing Linus and MacOSX executables… ---
**Author:** ![shawnteh1711](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@shawnteh1711](https://ask.bioexcel.eu/u/shawnteh1711)\ **Post date:** [November 26, 2017, 6:09pm UTC](https://ask.bioexcel.eu/t/error-when-running-wdir-encode-contacts-csh-structures-it0-acontacts-lis-acrb-contacts-pdb/640/3 "2017-11-26T18:09:55Z")
I checked the zone\_b F file and I just want to confirm, is it written using old-style fortran? I am a beginner in programming language. And i try to compile the zone\_b.f file using gfortran under cygwin but it comes with following error. ![image](https://dub1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/20e9c2794a08b53c0ceca194906c01a4923f4c1b.png) And when i try to compile with g77 compiler under DOS, it show another error. ![image](https://dub1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/df2aecb31533a5048e335c0f506a2ed0b8fc6815.png) Would appreciate if anyone can kindly explain. Thank you. ---
**Author:** ![shawnteh1711](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@shawnteh1711](https://ask.bioexcel.eu/u/shawnteh1711)\ **Post date:** [November 27, 2017, 6:46am UTC](https://ask.bioexcel.eu/t/error-when-running-wdir-encode-contacts-csh-structures-it0-acontacts-lis-acrb-contacts-pdb/640/4 "2017-11-27T06:46:02Z")
Currently, i am trying to run the code under Ubuntu but still having same error. zone\_b not found even when the zone\_b executable is in the directory. Please help as i have try a lot. ![image](https://dub1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/0fad6b5e7d254a5cd31ac699c7259255f5380f14.png) ---
**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:** [November 27, 2017, 11:03am UTC](https://ask.bioexcel.eu/t/error-when-running-wdir-encode-contacts-csh-structures-it0-acontacts-lis-acrb-contacts-pdb/640/5 "2017-11-27T11:03:18Z")
Hello, Sorry for those naive questions but they might help to narrow down the potential issues you’ve encountered: 1. Did you try to run the script directly? Something like: `$ANA_DIR/zone_b -50 -zA2,A2 test.pdb` (This assumes that you have a chain A with a residue id 2 in your PDB). It should assign the value 50 in the B-factor column of resid 2 of chain A in your test.pdb (it willl output it directly) 2. Out of curiosity, scripts are all executable? (`chmod a+x zone_b` to allow for execution) Thanks in advance, Mikael ---
**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 27, 2017, 6:21pm UTC](https://ask.bioexcel.eu/t/error-when-running-wdir-encode-contacts-csh-structures-it0-acontacts-lis-acrb-contacts-pdb/640/6 "2017-11-27T18:21:46Z")
The scripts are meant to run under `tcsh` or `csh` Did you source the `setup.csh` script as instructed? ---
**Author:** ![shawnteh1711](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@shawnteh1711](https://ask.bioexcel.eu/u/shawnteh1711)\ **Post date:** [November 27, 2017, 7:03pm UTC](https://ask.bioexcel.eu/t/error-when-running-wdir-encode-contacts-csh-structures-it0-acontacts-lis-acrb-contacts-pdb/640/7 "2017-11-27T19:03:16Z")
Yes, i am doing it under tcsh for source setup.csh ---
**Author:** ![shawnteh1711](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@shawnteh1711](https://ask.bioexcel.eu/u/shawnteh1711)\ **Post date:** [November 27, 2017, 7:17pm UTC](https://ask.bioexcel.eu/t/error-when-running-wdir-encode-contacts-csh-structures-it0-acontacts-lis-acrb-contacts-pdb/640/8 "2017-11-27T19:17:19Z")
May i ask what language does the zone\_b.linux used. As it is not view able when i open it. ---
**Author:** ![shawnteh1711](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@shawnteh1711](https://ask.bioexcel.eu/u/shawnteh1711)\ **Post date:** [November 28, 2017, 1:00am UTC](https://ask.bioexcel.eu/t/error-when-running-wdir-encode-contacts-csh-structures-it0-acontacts-lis-acrb-contacts-pdb/640/9 "2017-11-28T01:00:52Z")
1. I run the script zone\_b -50 -zA2,A2 3AOD-renumbered.pdb. It show zone\_b command not found as well. 3AOD-renumbered.pdb is the default pdb come with the tutorial with chain A and residue id 2. 2. i run the chmod a+x zone\_b. The command doest produce any error and statement. I check the properties of zone\_b, the file is executable. ![image](https://dub1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/c388dcb988f107aed8725fede65a44f082831bd5.png) ![image](https://dub1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/a8a29f9cd1a6496661ae1e4f67a6755bba678fdb.png) Would appreciate if can kindly explain. ---
**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 28, 2017, 8:39am UTC](https://ask.bioexcel.eu/t/error-when-running-wdir-encode-contacts-csh-structures-it0-acontacts-lis-acrb-contacts-pdb/640/10 "2017-11-28T08:39:09Z")
Did you try calling zone\_b with the full path to it? Did you source the setup.csh script as instructed? zone\_b.linux is a statically compiled fortran executable.