Do we need to rename the ligand's file names while preparing the input files for VPLP?

VFLP
#1

Dear All,

To prepare the input files for VFLP, Do we need to rename the ligand file name’s
( . smi ----> AAAA.0000 (xxxx) ) in input-file folder that names same as todo.all list file (AAAA.0000), located in the ~/templates or should we enter the files name’s (*.smi) to todo file ?.

I specified the collection folder as follows, the input files location is relative to tools folder.
(collection_folder=…/input-files/ligand-library)

and tested that whether my script is reading input files or not, By commenting out collection_folder line in all.ctrl.
(#collection_folder=…/input-files/ligand-library)

In both cases, the script prepare todo.all , todo.all.xxxx files in the ~ /VFLP-develop/workflow/ligand-collections/.

If I comment out collection folder, the script is not supposed to prepare the files in /VFLP-develop/workflow/ligand-collections/*******. since it is not reading the input files. Correct me, if i am wrong.

If you are runing with VFLP successfully, could you please share the protocol ( input-file preparation) here ?.

Thank you.

1 Like
#2

Dear all,
Looks like, don’t have to rename the ligand files names as per shell script. The job was started, but end-up with known error that posted earlier.

The next todo list will be used (todo.all.0003)
After (re)filling the todolists the queue 1-1-1 has 1000 ligands todo distributed in 1000 collections.
After (re)filling the todolists the queue 1-1-2 has 1000 ligands todo distributed in 1000 collections.
After (re)filling the todolists the queue 1-1-3 has 1000 ligands todo distributed in 1000 collections.
After (re)filling the todolists the queue 1-1-4 has 1000 ligands todo distributed in 1000 collections.
After (re)filling the todolists the queue 1-1-5 has 1000 ligands todo distributed in 1000 collections.

The todo lists for the queues were (re)filled in 45 second(s) (waiting time not included).
The waiting time was 303 second(s).

Starting job step 1 on host compt082.

nailgun/tools/
nailgun/tools/google-java-format/
nailgun/tools/google-java-format/LICENSE
nailgun/tools/google-java-format/README.txt
nailgun/tools/google-java-format/google-java-format-1.6-all-deps.jar
Error: Could not find or load main class com.martiansoftware.nailgun.NGServer
Caused by: java.lang.ClassNotFoundException: com.martiansoftware.nailgun.NGServer
Job step 1 is starting queue 1-1-1 on host compt082.
Job step 1 is starting queue 1-1-2 on host compt082.
Job step 1 is starting queue 1-1-3 on host compt082.
Job step 1 is starting queue 1-1-4 on host compt082.
Job step 1 is starting queue 1-1-5 on host compt082.
Error was trapped
Error in bash script one-step.sh
Error on line 307
Environment variables

#3

Hi @vas2201, could you please add some details on how you prepared the input data for VFLP? I’m trying to do the same but nothing goes to the output-files folder once the jobs are finished. I’m still confused about the directory structure for the VFLP input. I’ve got a bunch of smile files that I curated by hand.

  1. Can I just add smiles files as input-files/*.smi or do I need input-files/ligand-library/*.smi?
  2. Or do I need a deeper level hierarchy like tranche names? If yes, then how do I decide, which letters to use for defining the meta-tranche?
  3. Do I also need to make any changes in todo.all or anywhere else? If yes, what changes?

Thanks,
mnis

#5

Hi Mnis,

I am sorry and not active recently.
since i have so many issues with VFLP. I prepared ligand Libs using Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening. After that you have to use open-babel to convert the files in required format for VFVS.
all the best