[Chimera-users] Protonation of selected atoms ?

[Marek Maly]

Dear Elaine,

thanks for PROPKA advice, but it seems that
PPI dendrimer is still too "exotic" structure for this software
- see the attached results.

Anyway after the short experiment with "tutorial" 1hpx structure I am not  
sure
that this software physically adds/deletes hydrogen atoms to/from the  
molecular structure,
taking in account calculated pKa values and the desired pH value.

In fact it seems to me that there is no chance to provide pH value of the  
interest
here as the important input value for estimating the ionic states of the  
protonable
residues.

    Best wishes,

       Marek







Dne Thu, 28 Nov 2013 16:32:50 +0100 Elaine Meng <meng at cgl.ucsf.edu>  
napsal/-a:

> Hi Marek,
> You might also want to take a look at PROPKA, developed by the Jensen  
> group, University of Copenhagen:
> <http://propka.ki.ku.dk/>
>
> Although developed originally for proteins, it looks like it has been  
> extended to "ligands" as well.  I haven't tried it on nonproteins, but  
> there are some literature references on that page that discuss the  
> method and how it has been extended.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Nov 28, 2013, at 5:44 AM, Marek Maly wrote:
>
>> Dear Eric and Elaine,
>>
>> thank you very much for your help !
>>
>> My request comes from the fact that depending e.g. on pH
>> in general just the certain percentage of protonable groups
>> is really protonated. This for sure holds for "synthetic" polymers
>> but perhaps also for proteins.
>>
>> To adjust protonation states on proteins I am using H++ server
>> ( http://biophysics.cs.vt.edu/ ) which is the specialized/sofisticated
>> software e.g. to calculate ionic state of the protonable groups taking  
>> here
>> in account pH, dielectric constants (internal/external),  
>> micro-environment
>> of the protonable groups etc. Unfortunately this tool seems to works  
>> "just" for the proteins
>> (not for example for synthetic polymers or other molecules).
>>
>> So I appreciated the possibility to add hydrogens to the molecular  
>> structure in Chimera.
>>
>> Both advices (Elain's and Eric's) might be used to achieve desired  
>> partial protonation
>> of the molecular structure using actual chimera possibilities however  
>> depending on the size of the structure and depending on the percentage  
>> of the protonation and depending on the eventual additional  
>> requirements regrading  distribution of the protons between different  
>> molecular residues
>> (e.g. those containing primary amines, those containing secondary  
>> amines those containing tertiary
>> amines ...) it might be still more or less "dirty" manual work.
>>
>> So if may I suggest something for the future Chimera development, it  
>> would be perhaps the possibility
>> to protonate just the given percentage (e.g. with random distribution)  
>> of certain kind of protonable atoms (e.g. primary, secondary, tertiary  
>> amines , O atoms on COO groups ) which moreover belongs just to  
>> actually selected molecular part. Of course that regarding "steric  
>> clashes" etc. also the "non-selected" parts of the structure should be  
>> always considered in the process of protonation of the actually  
>> selected parts.
>>
>>   Best wishes,
>>            Marek
>


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