[Chimera-users] Need help in Coulombic surface coloring

Haresh Tukaram More htm211 at nyu.edu
Tue Jan 28 10:29:45 PST 2014


HI Elaine,

I tried to do that, but not able to add charges manually. I have attached a
PDB filer here with TFLE mutations. Can you please see if you can add
charges on it. I am unable to give charge to TFLE as all the time the
process stop at antechamber.exe and abruptly closes the chimera.

Thanks & Regards,
Haresh


On Tue, Jan 28, 2014 at 12:27 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Haresh,
> There is another issue you may wish to consider:  Add Charge will require
> adding hydrogens first, but then the molecular surface will be more
> "craggy" due to the additional small atoms. Here are instructions if you
> want to show the Coulombic ESP coloring on the less rugged surface
> calculated without hydrogens (as is usually done; radii automatically
> adjust to compensate):
>
> After adding hydrogens and charges:
> (1) when you use the Coulombic Surface Coloring tool, turn on the option
> to "Compute grid..."  (in my test just now I took the defaults for the other
> grid options)
>
> (2) delete the hydrogens, e.g. command: del H
>
> (3) use the "Surface Color" dialog that automatically appeared when you
> created the grid to color the main surface by electrostatic potential using
> the potential file (grid) you just created.  If you don't see that dialog,
> you can raise it using menu: Tools... Surface/Binding Analysis... Electrostatic
> Surface Coloring. The default name of that grid is Coulombic ESP.  (Do not
> use the Coulombic Surface Coloring dialog for coloring!  After the
> hydrogens with many positive charges have been deleted, mostly negative
> charges will be left, and you will get an incorrect very red surface using
> the Coulombic Surface Coloring dialog.)
>
> Normally the protein wouldn't have strange residues that require a
> separate charge calculation, and this circuitous process wouldn't be
> required.
> 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 Jan 27, 2014, at 6:56 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
>
> > Thanks a lot Elaine. I will try to work on it now and see if I can get
> any results.
> >
> > Regards,
> > Haresh
> >
> >
> > On Mon, Jan 27, 2014 at 12:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Haresh,
> > The Reply Log message (see the bottom part of what you sent) says there
> was a problem calculating the charges of your mutated residues and that you
> should try running Add Charge first, so that's what I would recommend.  Add
> Charge is in the menu under Tools.. Structure Editing, or can be run with
> command "addcharge".  It has two options for calculating the charges of
> nonstandard residues: AM1-BCC or Gasteiger.  Since the message shows there
> was a problem calculating using the AM1-BCC method on your mutated
> residues, I would try the Gasteiger method instead.
> >
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html
> >
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addcharge.html>
> >
> > Then, after you run Add Charge successfully, you can run Coulombic
> again.  It will automatically detect that the charges have already been
> calculated, and use those charges for calculating the ESP and coloring the
> surface.
> >
> > Actually I tried calculating charges for a single 5,5,5-trifluoroleucine
> residue by itself (in Chimera, can use "open pubchem:259832" to fetch it by
> PubChem CID)
> > <
> http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=259832&loc=ec_rcs>
> > ...and both methods, AM1-BCC and Gasteiger, worked fine; however maybe
> the calculation is more difficult in your structure where it sounds like
> the two mutated residues are treated together.
> >
> > I hope this helps,
> > 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 Jan 26, 2014, at 8:52 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
> >
> > > Hi,
> > > I tried to get the Coulombic surface coloring for one of the protein
> that I modified by removing certain residue at the C-termini and then
> mutated some residues to the non-natural amino acid 5,5,5-trifluoroleucine
> using Swisssidechin option. I am getting this error which I am not able to
> understand.
> > >
> > > Disabled GPU programs because a graphics driver bug
> > >   was encountered while compiling a vertex shader.
> > >
> > > #0, chain A: COMP
> > > #0, chain B: COMP
> > > #0, chain C: COMP
> > > #0, chain D: COMP
> > > #0, chain E: COMP
> > > C:\Program Files\Chimera 1.8.1\bin\mscalc.exe 1.400000 2.000000 1
> > > MSMSLIB 1.3 started on Local PC
> > > Copyright M.F. Sanner (March 2000)
> > > Compilation flags
> > >
> > > Surface CC TFLE.pdb, category main, probe radius 1.4, vertex density 2
> > >   22 connected surface components
> > >   Total solvent excluded surface area = 10393.6
> > >     component areas = 8599.46, 624.842, 225.9, 216.153, 81.7059,
> 54.8894, 54.839, 48.0624, 45.9525, 43.9588, 41.5667, 39.1204, 38.7549,
> 37.0513, 35.5418, 33.6712, 32.9167, 28.9293, 27.8262, 27.7523, 27.7319,
> 26.9429
> > >   Total solvent accessible surface area = 10372
> > >     component areas = 9971.67, 202.012, 92.2225, 70.7414, 13.8165,
> 4.12717, 3.62753, 3.24856, 2.597, 1.1866, 1.72654, 1.33137, 1.08737,
> 0.962375, 0.64812, 0.231422, 0.40193, 0.120068, 0.0570046, 0.0515394,
> 0.0674059, 0.0311705
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain A;
> guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain B;
> guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain C;
> guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain D;
> guessing terminii instead
> > > No SEQRES records for combination (#-2147483648.-2147483648) chain E;
> guessing terminii instead
> > > Chain-initial residues that are actual N terminii:
> #-2147483648.-2147483648 MET 27.A, #-2147483648.-2147483648 MET 27.B,
> #-2147483648.-2147483648 MET 27.C, #-2147483648.-2147483648 MET 27.D,
> #-2147483648.-2147483648 MET 27.E
> > > Chain-initial residues that are not actual N terminii:
> > > Chain-final residues that are actual C terminii:
> #-2147483648.-2147483648 TFLE 67.A, #-2147483648.-2147483648 TFLE 67.B,
> #-2147483648.-2147483648 TFLE 67.C, #-2147483648.-2147483648 TFLE 67.D,
> #-2147483648.-2147483648 TFLE 67.E
> > > Chain-final residues that are not actual C terminii:
> > > 424 hydrogen bonds
> > > Hydrogens added
> > > Charge model: AMBER ff12SB
> > > Assigning partial charges to residue TFLE+TFLE (net charge +0) with
> am1-bcc method
> > > Running ANTECHAMBER command: C:/Program Files/Chimera
> 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i
> c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.in.mol2 -fi mol2 -o
> c:\users\haresh~1.pol\appdata\local\temp\tmpipssqi\ante.out.mol2 -fo mol2
> -c bcc -nc 0 -j 5 -s 2
> > > (TFLE+TFLE)
> > >
> > > Cannot automatically determine charges for residue TFLE+TFLE;
> > > Run AddCharge tool manually to add charges and then rerun ESP
> > >
> > > Can someone please tell me a step by step procedure to make this work.
> > > Thanks & Regards,
> > > Haresh
> >
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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