From: Nikhil Maroli (scinikhil_at_gmail.com)
Date: Wed Aug 23 2017 - 10:07:59 CDT
On 22 Aug 2017 15:44, "Nikhil Maroli" <scinikhil_at_gmail.com> wrote:
Well, I use Discovery Studio, my suggestion is download it from here
<http://accelrys.com/products/collaborative-science/biovia-discovery-studio/visualization-download.php>
and load your protein-ligand system to DS. On the left panel you can
make unique name for ligand and save it to mol2. Now upload
protein-ligand file to charmm-gui (Make sure the naming in complex pdb
and mol2 files are same) then upload the mol2 in
PDB manipulation option .
Renaming Engineered Residues:
Rename *GOL* to Leave blank to remove
Has three membered ring Lowers the bomlev before reading the hetero
chain in case three membered ring is present
Rename *BOG* to Leave blank to remove
Has three membered ring Lowers the bomlev before reading the hetero
chain in case three membered ring is present
Rename *HOH* to Leave blank to remove
Has three membered ring Lowers the bomlev before reading the hetero
chain in case three membered ring is present
Upload CHARMM top & par for engineered res
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