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@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@h :8.T@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@cgl.ucsf.edu <mailto:chimera-users-request@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)
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Message: 1 Date: Wed, 16 Sep 2020 15:41:33 -0700 From: Eric Pettersen <pett@cgl.ucsf.edu> To: Jatin Kashyap <jk435@njit.edu> Cc: Chimera User Help <chimera-users@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@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@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@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote:
It's "addh" not "add H".
--Eric
On Sep 16, 2020, at 2:44 PM, Jatin Kashyap <jk435@njit.edu <mailto:jk435@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@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
?? Jatin Kashyap
On Sep 16, 2020, at 5:32 PM, Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@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@h :8.T@h".
--Eric
Eric Pettersen UCSF Computer Graphics Lab
> On Sep 16, 2020, at 2:10 PM, Jatin Kashyap <jk435@njit.edu <mailto:jk435@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@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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