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 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@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

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