[Chimera-users] AFTER DOCKING I AM SAVING THE PDB FILES, BUT IN THAT PDB FILE THE LIGAND AND RECEPTOR ARE HAVING THE SAME NAME

[Shinjini Ghosh]

I am sorry, but the above links did not help me.
Yes they are together in one model. But if suppose a receptor has NAD in it
, it shows in the residue region. But after docking the ligand name becomes
the same as the receptor. So it is difficult for me to show which ligand I
have used to dock.

I have attached an example pdb file.
Here both the ligand and receptor are in chain A and have the same name :
dock.pdb
and under "residue" my docked ligand is not coming. How to save a pdb file
(docked file) which considers the receptor and ligand separately in the
same PDB, like for example in the 3U31 file which I have attached (PDB file
downloaded from PDB) has NAD, gol, etc under residues. and when I am using
another software to check the interaction, it is showing the interactions
with all the residues. But this  "dock" PDB file which I made (after
docking) there is difficult to understand the interaction as it is showing
no ligand bound, since both of them are saved under the same name.



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08/07/20,
09:56:05 PM

On Fri, Aug 7, 2020 at 9:48 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Shinjini,
> It is unclear what name you are talking about.  There is a "model name",
> maybe the ligand and receptor are together in one model.  There is a "file
> name" of the saved PDB file.  There are "residue names," many different
> amino acids in the receptor, each one with its own name, and probably the
> ligand also has another different residue name.  Each atom also has an
> "atom name."
>
> If you want separate files, just select the atoms you want in one file,
> use menu: File ... Save PDB and choose the option to "save selected atoms
> only".   Then select the atoms you want in the other file, and use the same
> process to save another PDB file.  You can name each file whatever you want.
>
> Selecting atoms:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
>
> Saving PDB files:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
>
> If you want to change residue names or atom names, maybe you just want to
> text-edit the PDB file directly (not using Chimera).  Here is some
> explanation of PDB file format so you can understand how to edit the text.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html
> >
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Aug 7, 2020, at 7:37 AM, Shinjini Ghosh <shinjinighosh2014 at gmail.com>
> wrote:
> >
> > For analysis, I want to have a PDB file of let's say with the first
> docked ligand in chimera which I did with autodock vina. I was able to save
> and open it in chimera. But the receptor and the ligand are both having the
> same name which I am using to save my PDB file. How can I change the names
> of receptor and ligand in the PDB file so that it is considered as
> different molecules in that particular PDB file. I want to give two
> different names to the receptor and the ligand in that particluar PDB file.
> This I need for my project.
> > Please help me with this.
> > Thank you.
>
>

-- 
Shinjini Ghosh.
Student of Master of Science,
Biophysics and Molecular Biology'
Rajabazar Science College,
University of Calcutta.

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