[Chimera-users] substituting atoms

simon chapman rowanlodge19 at gmail.com
Wed Jan 17 04:33:18 PST 2018


Hello Eric and Elaine. Chance of earning a second pint of ginger beer if
you wish...

Simulations and analysis going very well, I have substituted all 12 oxygens
for sulphur. Each requires a new name: UNK I, UNK2 etc. Advice for
others...naming will only alow digits 1 to 9. so for 12 iterations, I used
zero and the original unappended "UNK". Which makes 12. I have also
successfully set production for 50000steps, equivalent to 8ps.

However, there appears to be an option for continuation from one run to a
subsequent one. I've tried for a few days now, but get the same error
message every time ('continuation2 attachment').  Changing file names as
described in the message doesn't work. It's probably something simple
(probably me in fact), but would really appreciate your comments.

Best wishes   Simon



On 10 January 2018 at 19:01, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> 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> 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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>>
>>
>
>
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