sai nitin wrote:
Hi all,
I have done complex (protein + ligand) complex from autodock software
using this complex im trying to follow
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html
tutorial
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..?
Whatever you're doing is changing the coordinates that you originally had. You
don't want to do that.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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