Docking with heteroatom included in protein pdb

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Docking with heteroatom included in protein pdb

Postby saharinku » Wed Jun 19, 2013 7:08 pm

Hi
I have using Pyrx for a while and I must say its a great tool and thus want to extend my thanks.
At this point I am trying to virtual docking of 100 ligand molecules . And I need the heteroatom NAD included in protein .pdbqt file.

But when i give the .pdb file and use Pyrx to convert it to .pdbqt file the NAD heteroatoms are deleted.

Attached is a sample .pdb file with NAD molecule(heteroatom) and I need it to converted to .pdbqt along with the NAD inside it.

Thus need help on how to make Pyrx not delete the NAD heteroatoms during conversion from .pdb to .pdbqt file.

Any help is greatly appreciated.

Best Regards
saharinku
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Re: Docking with heteroatom included in protein pdb

Postby sargis » Wed Jun 19, 2013 7:26 pm

Thanks for appreciating the hard work that went into making PyRx. I have implemented a feature in 0.9 version that provides an option to keep or remove non-standard residues (HETATM) - https://sourceforge.net/apps/trac/pyrx/milestone/0.9. If you have access to Linux, please try 0.9 there to see if this works for you.

Thank you for using PyRx!
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Re: Docking with heteroatom included in protein pdb

Postby saharinku » Wed Jun 19, 2013 8:33 pm

As I am using 0.8 in windows may I ask if there is a way to do it in this version.

Best
Rinku
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Re: Docking with heteroatom included in protein pdb

Postby saharinku » Tue Jul 23, 2013 1:33 pm

I installed Pyrx 0.9 and it works very fine. Thank you.
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Re: Docking with heteroatom included in protein pdb

Postby sargis » Tue Jul 23, 2013 5:07 pm

saharinku wrote:I installed Pyrx 0.9 and it works very fine. Thank you.

Thank you for the update. Glad to know PyRx 0.9 works fine with heteroatom included in protein pdb.
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Re: Docking with heteroatom included in protein pdb

Postby saharinku » Mon Aug 26, 2013 1:20 pm

Hi
I need a little help with this. I did flexible docking with a protein . So in the flex file are the flexible residues of protein information and then there is a a rigid.pdbqt file which has the rigid atoms coordinates for the protein. Thus when I did the docking with one of the ligand, i get the ligand001 _out.pdbqt output file(attachment) . In this file I don't see any thing on the ligand and its just the flexible residue atoms present in the output file. May Iask if something went wrong.
As attachment I am sending the test protein rigid.pdbqt, flex.pdbqt and ligand.pdbqt. In addition I am sending the output file I got from docking.

Any help is greatly appreciated.

Best
saharinku
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Re: Docking with heteroatom included in protein pdb

Postby oivalf_nix » Sat Oct 05, 2013 2:23 pm

Hi.

Your pdb file has a lot of errors. Probably this is the reason of the fail.
First of all, the formatting of the columns must be preserved. Columns from NAD 601 and 602 are displaced in your file.
You must edit your pdb file in order to change NAD and NH3 designations from ATOM to HETATM and also correct column orientation.
If you also change the chain designation of NAD from A, to C, like the rest of your protein, when you open the pdb in Pyrx and set chain C as macromolecule, Pyrx 0.9 will ask you what to do with NAD and NH3. You choose keep, just as Sargis said.

Regards,

Flavio
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