Hello.

1) Yes, you can batch LIGPLOT. Just have to do a small shell script that looks all your VS results as input for Ligplot. But keep in mind that you must have the ligand and receptor in only one file (I don't know which VS software you use.

2) The interaction is in a file named ligplot.txt. There you have HB mainchain-mainchain (M-M), sidechain-sidechain (S-S), mainchain-sidechain (M-S) and non-bonded contacts (NB). See the attached file for better information.

3) I think you can only change font style while using LIGPLUS (the GUI form of LIGPLOT).

Ricardo

Ricardo J Ferreira would you mind elaborating? I too am looking to find a way to batch process ligplot for many conformations of ligand + protein (for potentially hundreds of proteins). Furthermore, I would like to create my own output file (that’s not the LigPlot auto-generated diagram) that focuses on the amino acid residues that are involved with hydrophobic interactions with the protein. I do not know how I would be able to do this, and I am also unable to find the “LigPlot.txt” file you had alluded to above. Any help would be much appreciated!

Hi,

the script I use is this:

########################################################

# LIGPLOT

export ligdir='/opt/LigPlus/lib/exe_linux'

# LIST ALL FILES AND CREATE SUBDIRECTORIES

LISTFILES='*.pdb'

for f in $LISTFILES; do

b=`basename $f .pdb`

# CREATE SUBDIRECTORIES

mkdir ${b}

cp ${b}.pdb ./${b}/

# RUN HBADD, HBPLUS AND LIGPLOT FOR ALL FILES

cd ${b}

$ligdir/hbadd ${b}.pdb /opt/LigPlus/lib/params/components.cif -wkdir ./

$ligdir/hbplus -L -f ./hbplus.rc -h 2.90 -d 3.90 -N ./${b}.pdb -wkdir ./

$ligdir/hbplus -L -f ./hbplus.rc -h 2.70 -d 3.35 ./${b}.pdb -wkdir ./

$ligdir/ligplot ./${b}.pdb "-nLIG" $1 "-nLIG" $1 -wkdir ./ -prm /opt/LigPlus/lib/params/ligplot.prm

cd ..

done

########################################################

Then, you can create your own diagram from the "ligplot.sum" file within each directory. Probably, to better use with VS, you must add a script to create the input file for LigPlot from the separate protein and ligand files (standard PDF format), in which the ligand number is the one you feed into the LigPlot script.

Ricardo