Re: Creating psf file for ligand

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Thu Aug 24 2017 - 13:19:32 CDT

Dear Roshan,

the pdb files that you sent have the residue name set to UNK. Unless you
provide the rtf (topology) or a str (stream) file containing topology
information, psfgen or any other program depending on it (like QwikMD and
Autopsf) will not identify the residue properly.

As mentioned before, you can obtain the rtf and/or str files from
https://cgenff.paramchem.org/, and in the end, you need to feed psfgen, or
any other program that you use to build your system, with the files return
by the server.

Just a friendly warning, please inspect the penalties return by the cgenff
server as the topology and parameters may require further refinement.

I hope this helps

Best

Joao

On Thu, Aug 24, 2017 at 10:58 AM, Roshan Shrestha <roshanpra_at_gmail.com>
wrote:

> 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
>
>
>

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
jribeiro_at_ks.uiuc.edu
+1 (217) 3000380

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