[Chimera-users] Error "No MMTK name for atom "H" in standard residue “G""

[Jatin Kashyap]

Dear Chimera Community Members,

I am facing an error while minimizing a protein that have 5’ terminal phosphates attached to it. 
Chimera is showing the warning that AMBER is unable to parametrize the phosphates and if you do not delete it, 0 charges will be assigned to it. 
I selected the option not to delete it but then it throws error[1] on the following step. I am pasting my log below [2].

Thank you for helping me to understand this.

[1]
No MMTK name for atom "H" in standard residue “G"

[2]
Model 0 (7bv2_nsp12-7.pdb) appears to be a protein without secondary structure assignments.
Automatically computing assignments using 'ksdssp' and parameter values:
  energy cutoff -0.5
  minimum helix length 3
  minimum strand length 3
Use command 'help ksdssp' for more information.
Residues with incomplete side chains:
	LYS 98.A
	ASP 100.A
	ASP 218.A
	ASP 824.A
	GLU 50.C
Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True'
LYS 98.A: phi -78.3, psi 128.2 trans
Chi angles for LYS 98.A:
ASP 100.A: phi -70.1, psi -6.8 trans
Chi angles for ASP 100.A:
ASP 218.A: phi -127.8, psi 120.9 trans
Chi angles for ASP 218.A:
ASP 824.A: phi -92.0, psi 1.6 trans
Chi angles for ASP 824.A:
GLU 50.C: phi -60.9, psi -45.8 trans
Chi angles for GLU 50.C:
Applying LYS rotamer (chi angles: -62.5 -75.3 99.0 -88.6) to LYS 98.A
Applying ASP rotamer (chi angles: -67.2 -26.9) to ASP 824.A
Applying ASP rotamer (chi angles: -175.9 -11.3) to ASP 218.A
Applying ASP rotamer (chi angles: -70.6 -17.9) to ASP 100.A
Applying GLU rotamer (chi angles: -170.8 -83.2 -29.7) to GLU 50.C
No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain A; guessing terminii instead
No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain C; guessing terminii instead
No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain P; guessing terminii instead
No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain T; guessing terminii instead
Chain-initial residues that are actual N terminii: VAL 31.A, LYS 2.C, G 10.P, U 8.T
Chain-initial residues that are not actual N terminii: 
Chain-final residues that are actual C terminii: U 20.P, C 21.T
Chain-final residues that are not actual C terminii: THR 929.A, GLY 64.C
856 hydrogen bonds
Removing spurious proton from 'C' of THR 929.A
Removing spurious proton from 'C' of GLY 64.C
Hydrogens added
Charge model: AMBER ff14SB
Non-standard atom names:
	G H (G 10.P H)
	U H (U 8.T H)
Total charge for #0: -30.384
The following residues had non-integral charges:
	U 20.P -0.6919
	C 21.T -0.6919
Correct charges are unknown for 2 non-standard atom names in otherwise standard residues

Charges of 0.0 were assigned to the unknown atoms

1 model(s) had non-integral total charge
Details in reply log

No MMTK name for atom "H" in standard residue "G"


——
Jatin Kashyap 
New Jersey Institute of Technology

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