Running COACH standalone

[francescop]

Hi. I successfully installed ITASSER 5.2 and all the supporting librairies. When I try to run COACH on a protein I got the following errors, even if the computation seems to move forward:

[makemat] FATAL ERROR: Unable to open file psitmp.chk

Then the following are displayed:

cp: cannot stat 'psitmp.mtx': No such file or directory
cp: cannot stat 'pssm.txt': No such file or directory
cp: cannot stat 'psitmp.chk': No such file or directory

Could you please advise me how to fix that?

[jlspzw]

Dear user,

could you zip all your input files and attach them to the forum.

Best
IT Team

[francescop]

Sure. This is my input command line:
./runCOACH.pl -libdir /home/francesco/ITLIB/ -protname Albumin -model Albumin_predock.pdb -datadir ../../../Downloads/


Your setting for running COACH is:
-pkgdir = /home/francesco/Downloads/I-TASSER5.2
-libdir = /home/francesco/ITLIB
-protname = Albumin
-datadir = /home/francesco/Downloads
-outdir = /home/francesco/Downloads
-homoflag = real
-idcut = 1
-runstyle = serial
-LBS = true
-EC = true
-GO = true


And attached the protein.

[francescop]

Dear user,

could you zip all your input files and attach them to the forum.

Best
IT Team

Any suggestions? I updated what you required. Thanks.

[jlspzw]

Dear user,

We have checked and tested your case. Please see our running output of you case.

https://zhanggroup.org/COACH/output/coach_1.zip

1. COACH can only handle single-chain protein as input. While your input is a dimmer, please select either A chain or B chain from your Albumin_predock.pdb (see example Albumin_predock_A.pdb in our zip files)

2. please try to use -proname as the base name of your input PDB file. For example

../../I-TASSER5.2/I-TASSERmod/runCOACH.pl -libdir ~/ITlib/ -protname Albumin_predock_A -model Albumin_predock_A.pdb -datadir ./

Your setting for running COACH is:
-pkgdir = /xxx/I-TASSER5.2
-libdir = /xxx/ITlib
-protname = Albumin_predock_A
-datadir = /xxx/debug/coach
-outdir = /xxx/debug/coach
-homoflag = real
-idcut = 1
-runstyle = serial
-LBS = true
-EC = true
-GO = true

3. if you still have an issue after fixes 1 and 2, please see if the nr database in ITlib exists and is complete.

Let us know if you have any questions.

Best
IT Team

[francescop]

Thank you. I guess NR database was not downloaded. But if I run download_lib.pl I can see from the log that the attempt to connect to zhanggroup.org (zhanggroup.org)|141.213.137.249|:21... fails and NR db is not going to be dowloaded. Can you fix that? The server seems to not respond.

Best,

Francesco

[francescop]

It seems that the link ftp is wrong. I replaced with https and library subdirectory and now it seems to work.