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.
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.
Try to compile zone_b.f in the ana_script directory. We are only providing Linus and MacOSX executables…
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.
And when i try to compile with g77 compiler under DOS, it show another error.
Would appreciate if anyone can kindly explain. Thank you.
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.
Sorry for those naive questions but they might help to narrow down the potential issues you’ve encountered:
- 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)
- Out of curiosity, scripts are all executable? (
chmod a+x zone_b to allow for execution)
Thanks in advance,
The scripts are meant to run under
Did you source the
setup.csh script as instructed?
Yes, i am doing it under tcsh for source setup.csh
May i ask what language does the zone_b.linux used. As it is not view able when i open it.
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.
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.
Would appreciate if can kindly explain.
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.