[Chimera-users] dock prep multiple models

Eric Pettersen pett at cgl.ucsf.edu
Mon Jun 14 14:13:16 PDT 2010

On Jun 14, 2010, at 1:22 PM, Francesco Pietra wrote:

> Eric:
> Thanks. Headache adding hydrogen atoms (just as you mentioned addH)
> with my present system. Neither CHIMERA nor REDUCE were able to treat
> ASH/ASP HIP/HIE etc as I know from experiments, and software for pKa
> simulation also dropped. But it may be my fault.

As per the AddH documentation you should be able to get the  
protonation states you want if you specifically know those states  

Protonation States

AddH aims to generate protonation states reasonable at physiological  
pH. For example, hydrogens are not added to the phosphodiester  
moieties of DNA and RNA. By default, aspartic acid and glutamic acid  
sidechains are assumed to be negatively charged, while arginine and  
lysine sidechains are assumed to be positively charged (although other  
states can be attained). Two chemical moieties are treated as  
ambiguous at biological pH:

imidazoles such as histidine sidechains; histidine protonation states  
can be specified by the user or guessed by the method
terminal phosphates (the third ionization); if one P–O bond is at  
least 0.05 Å longer than the others around that same phosphorus atom,  
that oxygen will be protonated
Potentially ambiguous or rare (shifted-pKa) protonation states,  
especially in binding sites and nonstandard residues, should be  
verified and corrected as needed. For example, extra hydrogens can be  
deleted, and atom types can be edited (before hydrogen addition) with  
setattr or Build Structure.

That last part could probably use an example.  Let's say you know that  
the asparagine which is residue 39 in chain A should have atom OD1  
protonated.  Changing the atom type to O3 (from O2-) [before AddH]  
would accomplish that:

setattr a idatmType O3 :39.a at od1

If you don't know specifically which oxygen should be protonated, this  
may not be a big help.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

> As to the dockprep with either multiple pdb file, or single files
> followed by "cat", it seems to me now that the latter is advantageous,
> One can combine single-molecule mol2 files at will, and modify one or
> more mol2 files without repeating the whole calculation.
> francesco
> On Mon, Jun 14, 2010 at 8:29 PM, Eric Pettersen <pett at cgl.ucsf.edu>  
> wrote:
>> On Jun 14, 2010, at 10:48 AM, Francesco Pietra wrote:
>> With the combined pdb file,  does dockprep operate on single  
>> molecules
>> one after the other, so that it will not encounter obstacles even for
>> many (more complex) ligands?
>> I think this will be okay.  Chimera ignores sibling submodels (e.g.  
>> #0.2 is
>> a "sibling" of #0.1) when adding hydrogens so you will be okay if  
>> all your
>> ligands come from one file.
>> --Eric
>>                         Eric Pettersen
>>                         UCSF Computer Graphics Lab
>>                         http://www.cgl.ucsf.edu

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