Hi Eric,
Just for the clarification I am double checking it here, first I loaded the structure > del H > add H > del :10.P@h :8.T@h > minimize (while deselecting the add hydrogen option).
But it is throwing the error [1].
[1]
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.
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
852 hydrogen bonds
Removing spurious proton from 'C' of THR 929.A
Removing spurious proton from 'C' of GLY 64.C
Hydrogens added
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 ASP rotamer (chi angles: -67.2 -26.9) to ASP 824.A
Applying LYS rotamer (chi angles: -178.9 71.3 178.8 68.6) to LYS 98.A
Applying ASP rotamer (chi angles: -175.9 -11.3) to ASP 218.A
Applying GLU rotamer (chi angles: -170.8 -83.2 25.9) to GLU 50.C
Applying ASP rotamer (chi angles: -70.6 -17.9) to ASP 100.A
Charge model: AMBER ff14SB
Total charge for #0: -32.172
The following residues had non-integral charges:
LYS 98.A -0.6068
ASP 100.A -1.0636
ASP 218.A -1.0636
ASP 824.A -1.0636
GLU 50.C -0.9909
U 20.P -0.6919
C 21.T -0.6919
1 model(s) had non-integral total charge
Details in reply log
Residue #0:98.A (LYS/lysine) is missing atoms H_gamma_3, H_epsilon_2, H_zeta_3, H_delta_2, H_epsilon_3, H_alpha, H_beta_3, H_gamma_2, H_delta_3, H_beta_2, H_zeta_1 and H_zeta_2
Hi Jatin,
I you don't delete those phosphates, then Chimera will add spurious protons to them, which is what is causing the problem. In order to get this to work, you will have to run Add Hydrogens "by hand" before your minimization, delete the spurious protons, and then run your minimization -- being careful to skip adding hydrogens as part of the minimization process.
The command (Favorites→Command Line) to delete the unwanted protons in your case is "del :10.P@h :8.T@h".
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
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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