[Chimera-users] substituting atoms

simon chapman rowanlodge19 at gmail.com
Wed Jan 10 04:09:37 PST 2018

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

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> 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> 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> 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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