[Chimera-users] Need help in Coulombic surface coloring

[Haresh Tukaram More]

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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