[Chimera-users] Chimera-users Digest, Vol 209, Issue 27
Eric Pettersen
pett at cgl.ucsf.edu
Thu Sep 17 10:10:32 PDT 2020
Since you decided to retain the terminal phosphate and therefore charges of 0.0 were assigned to those atoms, you would expect the total charge for those residues and the overall structure to not be integral.
--Eric
> On Sep 16, 2020, at 5:08 PM, Jatin Kashyap <jk435 at njit.edu> wrote:
>
> Eric,
>
> Following are steps I followed: load the structure> del H > run Dock Prep(Add Hydrogen - ticked, Write Mol2 - unticked) > del :10.P at h :8.T at h > minimize (while deselecting the add hydrogen option)
>
> I got a warning that I am not sure about. I am pasting the log below[1], can you please confirm that I followed the correct steps and warning can be ignored in the log.
>
> [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.
> 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: -70.6 -17.9) to ASP 100.A
> Applying GLU rotamer (chi angles: -170.8 -83.2 -29.7) to GLU 50.C
> Applying ASP rotamer (chi angles: -175.9 -11.3) to ASP 218.A
> 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 incomplete side chains
> Charge model: AMBER ff14SB
> Total charge for #0: -30.384
> The following residues had non-integral charges:
> U 20.P -0.6919
> C 21.T -0.6919
> 1 model(s) had non-integral total charge
> Details in reply log
>
> Using main parameter file parm10.dat modified by heme-iron.frcmod, frcmod.ff14SB, frcmod.ionsjc_tip3p
> Initial energy: -45283.236153 kJ/mol
> Step 12
> Potential energy: -58447.379716, Gradient norm: 758.031360
> Updated 15035 atoms. RMSD: 0.037342
> Finished 10 of 100 steepest descent minimization steps
> Step 12
> Potential energy: -64213.179928, Gradient norm: 362.328469
> Updated 15035 atoms. RMSD: 0.018132
> Finished 20 of 100 steepest descent minimization steps
> Step 12
> Potential energy: -65930.345155, Gradient norm: 417.614654
> Updated 15035 atoms. RMSD: 0.012606
> Finished 30 of 100 steepest descent minimization steps
> Step 12
> Potential energy: -67901.748990, Gradient norm: 190.328174
> Updated 15035 atoms. RMSD: 0.010435
> Finished 40 of 100 steepest descent minimization steps
> Step 12
> Potential energy: -68928.640793, Gradient norm: 79.670023
> Updated 15035 atoms. RMSD: 0.007430
> Finished 50 of 100 steepest descent minimization steps
> Step 12
> Potential energy: -70504.551913, Gradient norm: 192.974949
> Updated 15035 atoms. RMSD: 0.016225
> Finished 60 of 100 steepest descent minimization steps
> Step 12
> Potential energy: -71243.383589, Gradient norm: 95.907393
> Updated 15035 atoms. RMSD: 0.006255
> Finished 70 of 100 steepest descent minimization steps
> Step 12
> Potential energy: -71661.708391, Gradient norm: 193.911209
> Updated 15035 atoms. RMSD: 0.006283
> Finished 80 of 100 steepest descent minimization steps
> Step 12
> Potential energy: -72255.311758, Gradient norm: 199.037193
> Updated 15035 atoms. RMSD: 0.007288
> Finished 90 of 100 steepest descent minimization steps
> Step 12
> Potential energy: -72873.927407, Gradient norm: 84.768251
> Updated 15035 atoms. RMSD: 0.005517
> Finished 100 of 100 steepest descent minimization steps
>
> Step 12
> Potential energy: -79350.452189, Gradient norm: 206.369396
> Updated 15035 atoms. RMSD: 0.114423
> Finished 10 of 10 conjugate gradient minimization steps
>
>
> ——
> Jatin Kashyap
>
>
>> On Sep 16, 2020, at 6:41 PM, chimera-users-request at cgl.ucsf.edu <mailto:chimera-users-request at cgl.ucsf.edu> wrote:
>>
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>> Today's Topics:
>>
>> 1. Re: Error "No MMTK name for atom "H" in standard residue ?G""
>> (Eric Pettersen)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 16 Sep 2020 15:41:33 -0700
>> From: Eric Pettersen <pett at cgl.ucsf.edu>
>> To: Jatin Kashyap <jk435 at njit.edu>
>> Cc: Chimera User Help <chimera-users at cgl.ucsf.edu>
>> Subject: Re: [Chimera-users] Error "No MMTK name for atom "H" in
>> standard residue ?G""
>> Message-ID: <9B74E727-F918-4A68-9E48-83F05E6B329E at cgl.ucsf.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Ah I see. Because you also have missing side chains you have to do things a little differently. Namely run Dock Prep (Tools?Structure Editing?Dock Prep) first, keeping "Add hydrogens" on but "Write Mol2" off; then use the delete command to delete the two unwanted protons; then run Minimize.
>>
>> --Eric
>>
>>> On Sep 16, 2020, at 2:54 PM, Jatin Kashyap <jk435 at njit.edu> wrote:
>>>
>>> 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 <mailto: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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
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>>>>>>
>>>>>
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>> End of Chimera-users Digest, Vol 209, Issue 27
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