[Chimera-users] Need help in Coulombic surface coloring

Tue Jan 28 14:43:37 PST 2014

Hi Elaine,

Yes I did exactly the way you explained and it is working now.

I have another question. I need to add some 14 residues on N-termius of the
protein which I did using the addaa command. However, I am unable to
simulate its secondary structure using ksdssp. I am not sure how to run
this command in command line. Or am I doing something wrong in terms of
predicting the structures.

Can you please let me know what do I need to do in terms of getting the
structure of protein after addsing residues on N-terminus.

Thanks,
Haresh

On Tue, Jan 28, 2014 at 2:46 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> No, don't use 9 for the charge of TFLE!  Total charge is including the
> whole protein.  Presumably TFLE  charge is 0, i.e., it is not a charged
> sidechain.
>
> Also you should delete hydrogens and then use Surface Color,  as in my
> previous instructions.
> Elaine
>
> On Jan 28, 2014, at 11:37 AM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
>
> > 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
> > > >
> > > >
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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