[Chimera-users] Need help in Coulombic surface coloring

[Haresh Tukaram More]

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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