GROMACS version: gmx, version 2021.4
I’m following the Protein-Ligand Complex tutorial .VMD .
I use the output from these commands :
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_10.tpr
gmx mdrun -deffnm md_0_10
Especially these two files:
md_0_10.gro
md_0_10.xtc
And with this VMD setting:
At best I can get is only the receptor (protein) but not the ligand bound to it.
How can I also show ligand in the binding?
-Sca
Specify its residue name (resname). This is a VMD question and is better suited to their mailing list.
1 Like
rpsingh
December 25, 2021, 12:27pm
3
Create Rep in VMD. Enter “resname XYZ” (do not include the quotes; replace XYZ with your ligand residue name). You can also play around with other options like “not protein not water”, resid, etc. See the VMD manual for more instructions.
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Thank you. That answered my question.
This is from a quick and dirt tutorial
# Create vmd.tcl file
cat << EOF >| vmd.tcl
display projection Orthographic
display rendermode GLSL
mol modselect 0 0 protein
mol modstyle 0 0 NewCartoon 0.300000 10.000000 4.100000 0
mol modcolor 0 0 Structure
mol addrep 0
mol modselect 1 0 noh and resname DMP
mol modstyle 1 0 Licorice 0.300000 12.000000 12.000000
mol modcolor 1 0 Type
color Type C white
mol addrep 0
mol modselect 2 0 noh same resid as within 8 of resname DMP
mol modstyle 2 0 Licorice 0.200000 12.000000 12.000000
mol addrep 0
mol modselect 3 0 noh same resid as within 8 of resname DMP
mol representation Licorice 0.200000 12.000000 12.000000
mol modstyle 3 0 HBonds 3.000000 20.000000 1.000000
mol modcolor 3 0 ColorID 0
mol modstyle 3 0 HBonds 3.000000 20.000000 6.000000
mol modcolor 3 0 ColorID 4
mol smoothrep 0 0 5
mol smoothrep 0 1 5
mol smoothrep 0 2 5
mol smoothrep 0 3 5
EOF
# Visualise with VMD
vmd md.gro md.xtc -e vmd.tcl
You need to adapt the ligand name obviously and, likely, other features. It’s worth investing time in VMD tcl commands IMO.
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