From: Roshan Shrestha (roshanpra_at_gmail.com)
Date: Thu Aug 24 2017 - 12:58:07 CDT
Nikhil,
I have attached both .pdb and .mol2 formats of the ligand which you
can check in here. In Quick MD setup, I uploaded the pdb file of the
ligand, then in Model/Chain selection option, I checked both Read all
models and Hetero Type. Now, I am having a bit of problem in Reading Hetero
Chain options, I used CHARMM General Force Field to generate CHARMM top &
par files option to upload .mol2 file, but still error persists. Can you
please check my results ?
Thanks
On Wed, Aug 23, 2017 at 8:52 PM, Nikhil Maroli <scinikhil_at_gmail.com> wrote:
>
>
> 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
>
>
>
-- Roshan Shrestha M.Sc (Physics) Central Department of Physics,Tribhuvan University Kathmandu,Nepal
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