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