[Chimera-users] Need help in Coulombic surface coloring

Tue Jan 28 11:37:35 PST 2014

Hi Elaine,

Finally!! it worked. In the reply log it shows following

Charges for residue TFLE determined
Assigning partial charges to residue CL (net charge -1) with gasteiger
method
Total charge for #0: 9.000

So i should use +9 charge for TFLE and TFLE+TFLE? I did that and now able
to get the electrostatic surface potential. The way I did is as follows

1. AddH
2. Add charge
3. Select surface of protein
4. Select coulombic surface coloring command and selected the grid option.
5. Next the surface color box opened and I selected color option.
6. Once it is done I removed hydrogen by del H

and I got the protein with electrostatic surface potential.

I hope now this is correct.

Regards,
Haresh

On Tue, Jan 28, 2014 at 1:44 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Haresh,
> If you use "Gasteiger" instead of "AM1-BCC" in the Add Charge dialog as
> suggested in my first reply, it works (at least for me, but I'm pretty sure
> it will for you too)!
> Elaine
>
> On Jan 28, 2014, at 10:29 AM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
>
> > 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
> > >
> > >
>
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