ADL: add hydrogens at certain pH.doubts..!! is it true? and necessary?

Miguel Quiliano Meza qilime at
Fri Mar 7 08:36:17 PST 2008

Dear Dockers.

I have doubts about add hygrogens at certain pH. According G. Morris (Also Biology, Chemistry, etc):

A related point to consider is the protonation state of all your 
 ionisable side chains: this will be determined by the pH and salt 
 concentrations, and you should look into pKa calculations.

to achieve that goal I added hygrogens with the server:

It works very well.. but the problem is when your protein has a LIGAND (another protein, cofactor..etc) because in that case 
is in beta version.

In my case my protein is a flavoenzime (FAD) and I want to try it in their oxidized state. So I try out with the server.
apparently all the outputs are OK.. However ADT:

1)Detects non integral charges (28 residues)
2) doesnt find some hydrogen bonds in FAD (in others 3D programs like CHIMERA,SPDviewer all bonds are ok)
3) As a result of this some oxigens in FAD have zero charge.

so I tried to fix these problems according the LIST:
1) You can solve the non-integral charge issue by clicking on
Edit->Charges->Check totals on residues.

2)If all the atoms in the macromolecule already have charges, ADT will not 
change the charges....  Solve this problem by setting up the atomic 
charges before you choose the macromolecule using 
Grid->Macromolecule->Choose Macromolecule

What you need to do is to assign charges to your protein after you have 
read it in and added all hydrogens to it....
This is complicated because you'll need to add both gasteiger charges 
and Kollman charges to each atom then set the charges of the 'hetatm' 
atoms to the gasteiger set ** ....PLUS you must add whatever charge you 
want for the iron atom(s) separately...  and all of this BEFORE you 
select your protein to be the macromolecule for the autogrid calculation...

Try these steps and let me know if you have problems or questions:

1. start ADT
2. load editCommands module (File->LoadModule)
3. read in your protein using File->Read Molecule (buildBondsByDistance 
if this doesn't happen automatically)
4. add all hydrogens (Edit->Hydrogens->Add)
5. compute gasteiger charges (Edit->Charges->Compute Gasteiger)
6. add Kollman charges (Edit->Charges->Add Kollman Charges)***

At this point, all the atoms in your protein have Kollman charges which 
are 0.0 for the non-standard amino-acid atoms (and for nonpolar 
The next step is to select the non-standard amino-acid atoms and set 
their charges to the gasteiger charge values they already have....

7. Open the python shell by clicking on the green snake icon located 
below the File button and above the "PCOM:" label
8. Type each of the following lines at the >>> prompt
hetatms = mv.allAtoms.get(lambda x:x.hetatm==1)

this should result in selecting all the hetatms in your protein...
9. set the charges on these selected atoms to their 'gasteiger' charge 
value by setting their chargeSet*** to gasteiger
Edit->Charges->Set Charge Field.... click on the button next to 
'gasteiger' and click OK

well.. Until now I have the same problem.. On the other hand I found some papers about proteins with FAD but they only said
"the partial charges were placed using GROMACS keeping FAD in an oxidized state.. (maybe they first added all hydrogens and then deleted to obteined oxidized state.. by hand) 
In conclusion.. my questions are:
1) have you ever used this kind of server..?? for add hydrogens, with ligands (FAD,NADPH, etc...)
2) what can i do? FAD by hand ??? add> hydrogens  and then delete..

finally I owe you an apology for my big question. so I would be very grateful if someone can help me with solutions or

thanks in advance.


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