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

Wed Sep 16 14:54:35 PDT 2020

I am sorry for the confusion. Actually I did that step by GUI options (Tools>Structure Editing>AddH). But I did it again by issuing “addh” from command line along with other steps.
But still I am getting the same error.

——
Jatin Kashyap 

> On Sep 16, 2020, at 5:49 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> It's "addh" not "add H".
> 
> --Eric
> 
>> On Sep 16, 2020, at 2:44 PM, Jatin Kashyap <jk435 at njit.edu <mailto:jk435 at njit.edu>> wrote:
>> 
>> Hi Eric,
>> 
>> Just for the clarification I am double checking it here, first I loaded the structure > del H > add H > del :10.P at h :8.T at 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 
>> 
>> 
>> ——
>> Jatin Kashyap 
>> 
>> 
>>> On Sep 16, 2020, at 5:32 PM, Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
>>> 
>>> 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 at h :8.T at h".
>>> 
>>> --Eric
>>> 
>>> 	Eric Pettersen
>>> 	UCSF Computer Graphics Lab
>>> 
>>> 
>>>> On Sep 16, 2020, at 2:10 PM, Jatin Kashyap <jk435 at njit.edu <mailto:jk435 at njit.edu>> wrote:
>>>> 
>>>> 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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>>> 
>> 
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