[gmx-users] Protein ligand molecular dynamics simulation

sai nitin sainitin7 at gmail.com
Mon Apr 16 17:01:36 CEST 2012

Hi all,

I have done complex (protein + ligand) complex from autodock software using
this complex im trying to follow


But when i take complex structure directly from autodock result and run
PDB2GMX it will give error because it is not recognizing ligand topology
which is in complex structure.
Then i followed justin tutorial took protein alone and applied Charmm27
Force field and used generate ligand topologies using Swissparam tool (
http://swissparam.ch/) when i do Editconf and created cubic box ligand is
going away from protein.

Actually my main task to place ligand in paraticular binding site in my
protein and perform molecular dynamics.

Can any body tell me how to do this..?

Thanks in advance


Sainitin D
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