[Chimera-users] Need help in Coulombic surface coloring

[Elaine Meng]

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