Docking failing randomly when docking custom ligand library with custom proteins

VFVS VFVS 1
#1

Hey Guys,

I have setup VFVS1 and have docked multiple (49) ligands with my protein, but most of the time it get failed by throwing the following error in the queue file of my workflow:
…/workflow/job-files/sub/one-queue.sh: line 194: 1711718346 * 1000 + 057134389: value too great for base (error token is “057134389”)

In the above error the pipeline was able to dock only 20/49 ligands and gave the above error.
But when i run the pipeline again, either it dock with less than 20 ligands or with more than 20 ligands or can also be docked with all the ligands.
I am unable to solve this issue can anyone help me out on this?

VFVS problems in exit
#2

Hi Haroon

Your problem sounds familiar. I fixed it by changing three variables in one-queue.sh:

183:#    docking_start_time_ms=$(($(date +'%s * 1000 + %-N / 1000000')))
184:    docking_start_time_ms=$(echo "$(date +%s)000 + $(date +%N) / 1000000" | bc)
195:#    docking_total_time_ms="$(($(date +'%s * 1000 + %-N / 1000000') - ${docking_start_time_ms}))"
197:    docking_total_time_ms=$((timestamp - docking_start_time_ms))
862:#            start_time_ms=$(($(date +'%s * 1000 + %-N / 1000000')))
863:            start_time_ms=$(echo "$(date +%s)000 + $(date +%N) / 1000000" | bc)

The line numbers won’t correspond exactly to your line numbers. Simply search for the three variables by > grep -n start_time_ms one-queue.sh

This solved the problem for me.

Best, Oliv

#3

Thanks oliver for the help, it is docking properly now.

#4

Hi har_vf,

Can I ask why you would attempt to dock such a small number of ligands using VFVS?

Was this simply a test case?

Kind regards,

Sorin

#5

Hello Sorin,
Yes it was for test case, but now as i have set it up, I am using VFVS for docking on large scale.