Vina understands multithreading, and will automatically spawn four threads on a four-core machine. This means that you are better-off asking directly for -N1 (ie. one node) and avoid complications. To submit a job

• Collect all your files in a directory. For example :

-rw------- 1 glykos glykos 253037 Mar  8 11:26 4HD5.pdbqt
-rw------- 1 glykos glykos   1474 Mar  8 11:26 GlcNAc.pdbqt
-rw------- 1 glykos glykos    152 Mar  8 11:26 example.cfg

• Prepare a submission script, let's say script.sh containing the following:

#!/bin/tcsh 
 
vina --config example.cfg
 
exit

• Submit it to the non-cuda partition of the cluster :

sbatch -p noncuda -n4 -N1 script.sh

Results will appear in the current directory, the output will be contained in the file slurm-*.out, and the directory will look something like this after job completion :

-rw------- 1 glykos glykos 253037 Mar  8 11:26 4HD5.pdbqt
-rw------- 1 glykos glykos   1474 Mar  8 11:26 GlcNAc.pdbqt
-rw------- 1 glykos glykos    152 Mar  8 11:26 example.cfg
-rw-r--r-- 1 glykos glykos  13869 Mar  8 11:40 out.pdbqt
-rw-r--r-- 1 glykos glykos     46 Mar  8 11:33 script.sh
-rw-r--r-- 1 glykos glykos   1792 Mar  8 11:40 slurm-3040.out