[phenixbb] Adding H atoms onto ligand

[Young-Jin Cho]

Thanks a lot Nigel,
I could generate new .cif file. Then I need to combine this ligand information while I am adding H atoms to model.pdb (protein+ligand). when I simply type "phenix.ready_set model.pdb" it will wrongly generate strange.pdb file. My question is how I can add this new geometry information (.cif file) while adding H atoms into modle.pdb file to make protein and ligand has H atoms in correct way.

Thanks again in advace.

YoungJin 


----- Original Message -----
From: "Nigel W Moriarty" <NWMoriarty at lbl.gov>
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
Sent: Tuesday, June 16, 2009 12:18:50 PM GMT -05:00 US/Canada Eastern
Subject: Re: [phenixbb] Adding H atoms onto ligand


YoungJin 

If you opened the CIF in REEL you can right-click on the P-N bond and change the order to single. You can then use the menu Action -> Build -> Add Atom to add a hydrogen to the nitrogen by clicking on the nitrogen. 

Nigel 

On 6/16/09 9:03 AM, Young-Jin Cho wrote: 

Thanks Nigel,
I opened ANP and truncated the terminal PO3 and ran phenix.ready_set.  When I opened through phenix.reel, N atom has double bond to PB, thus has only one H atom, which I thought it should be single bond thus has two H atoms like any N6 of adenine.

So if you can tell me how I can handle to put correct geometry, it will be great.

Cheers,
YoungJin

----- Original Message -----
From: "Nigel W Moriarty" <NWMoriarty at lbl.gov> To: "PHENIX user mailing list" <phenixbb at phenix-online.org> Sent: Tuesday, June 16, 2009 11:21:18 AM GMT -05:00 US/Canada Eastern
Subject: Re: [phenixbb] Adding H atoms onto ligand

Young-Jin

You need to check that you and the PDB ligand database are talking about 
the same thing.  You can see what the ligand ANP is by

phenix.reel --chemical-components=ANP

If you have the non-hydrogen atoms of your truncated ligand, 
phenix.ready_set will add the hydrogens and may even add the correct 
number of hydrogens to the terminal nitrogen. But what about its name?  
I would recommend find the three-letter code that corresponds to your 
ligand.

Nigel

On 6/15/09 7:01 PM, Young-Jin Cho wrote: 

Let me excuse to post another similar issue.
I was now modifying AMPPNP ('ANP' in its library name). Although it came from coot/ccp4 library, phenix does not recognize so I had to generate .cif file from the pdb.
 As it turned out AMPPNP is hydrolyzed in the crystal having AMPPN (terminal Phosphate group needs to be removed), I made from coot (simply deleted  atoms) and made another .cif file. One question what I have now is while I am adding H atoms into a whole molecule, how I can add H atoms onto terminal AMPPN (N atom). Unlike ATP case, it is very certain that terminal N atom should have 2 H's.  I did Molprobity as in the general case to add H atoms, but it didn't make it.

Another questions is how I can remove H atoms from the pdb file. I did "phenix.refine model.pdb remove="element H" but got a message as below:
Processing inputs. This may take a minute or two.
Sorry: Ambiguous parameter definition: remove = element H
Best matches:
  refinement.refine.occupancies.remove_selection
  refinement.geometry_restraints.remove.angles
  refinement.geometry_restraints.remove.dihedrals
  refinement.geometry_restraints.remove.chiralities
  refinement.geometry_restraints.remove.planarities

Thanks in advance,

YoungJin


ps. Tanks Nat!
_______________________________________________
phenixbb mailing list phenixbb at phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb 
-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov Web   : CCI.LBL.gov 
_______________________________________________
phenixbb mailing list
phenixbb at phenix-online.org
http://www.phenix-online.org/mailman/listinfo/phenixbb