[Chimera-users] substituting atoms

[Eric Pettersen]

Great!  If we’re in the neighborhood I’ll take a pint of ginger ale. :-)

—Eric

> On Jan 10, 2018, at 4:09 AM, simon chapman <rowanlodge19 at gmail.com> wrote:
> 
> Hello Elaine and Eric. Thankyou for the prompt reply....and I'm very impressed! Eric's suggestion #2 worked!
> 
> I assumed the protonation was OK as I ran the PDB downloaded structure through a protonation webserver (H++).  So I just changed the name of the novel substitution. It looks like additional alterations will also need renaming: I ran the next substitution in the incremental progression( #5) as "UNK3",and that is just about to complete. 
> 
> I am especially pleased as the data are definitely tending to support my hypothesis. You will acknowledged in the Methodology section of my dissertation.
> 
> So, thanks again. There's a charming 14th century pub just down the lane from me...buy you both a pint next time you're passing through
> 
> Best wishes   Simon
> 
> On 9 January 2018 at 19:31, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
> Hi Simon,
> 	Everything Elaine says is true.  I do have some last ditch suggestions for you though.  One thing is that the fourth guanine differs in protonation state from the others in that the fourth one either has or lacks an HO3’ whereas the others don’t.  You should investigate why this is the case.  The two possibilities are then:
> 
> 1) The protonation difference is an error.  You would need to correct the structure so that all four guanines start with the same protonation.
> 2) For some reason the protonation difference is okay.  You then need to give the modified version of the fourth guanine a different name from the others, e.g. “UK2” instead of “UNK”.  Not guaranteeing this will work, but it might.
> 
> —Eric
> 
>  	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
> 
> On Jan 9, 2018, at 10:24 AM, Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> wrote:
>> 
>> Hi Simon,
>> I think you may be stretching the tools beyond their intended purposes: Chimera’s minimization, molecular dynamics interface, and automatic parametrization of nonstandard residues with Antechamber are meant to provide relatively simple access to such calculations by noncomputational scientists, given the large learning curves of dedicated simulation packages like GROMACS, AMBER, etc. These tools can be highly useful to clean up structures or suggest additional reasonable conformations. However, they are not meant for precise quantification of energies or for very long simulations, especially not in conjunction with nonstandard residues with parameters estimated by Antechamber.  The Gasteiger charges are very quick-and-dirty, so I would caution against overinterpreting simulations that employ them.  Further, Antechember is meant to cover most small organic molecules but not every possible molecule.
>> 
>> It seems that the modified UNK residues fall into two structural types (as per the “specify net charges” dialog), and that one (maybe just the 4th?) fails in parametrization by Antechamber, and then the Solvate or Add Ions tool cannot find some parameter needed for its calculation. These tools come from the Ambertools package even though they are included with Chimera and Chimera has interfaces to them.  I don’t know exactly what the problem is, nor do I have a solution, sorry.  
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>>> On Jan 9, 2018, at 1:30 AM, simon chapman <rowanlodge19 at gmail.com <mailto:rowanlodge19 at gmail.com>> wrote:
>>> 
>>> Hello Elaine, sorry to bother you again.
>>> 
>>> Chimera has been a real treat so far, but I have hit a problem. I've struggled for a week now, and finally given up!
>>> 
>>> I am incrementally substituting S for O on four guanines in a regular complex. 3 substitutions work fine in a simulation and producing very encouraging data (attachment 1) But 4 substitutions (attachment 2) triggers a load of error messages. The first is attachment 3. After solvation, attachment 4 appears and the solvation box is removed if neutralising ions are added. If ions not added, attachment 5 warning appears.  Not sure if attachment 6 is relevant.
>>> 
>>> Hope you can help/advise?
>>> 
>>> Best wishes   Simon
>>> 
>> 
>> 
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> 

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