those are also error which I have obtained today from MDs plugin of chimera while trying to prepare the structures to optimization. No MMTK name for atom "HA" in standard residue "LEU" No SEQRES records for MD_polariz_ions22.pdb (#0.1) chain A; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.1) chain B; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.1) chain C; guessing terminii instead Chain-initial residues that are actual N terminii: #0.1 GLY 17.A, #0.1 GLN 1.B, #0.1 MET 1.C Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #0.1 THR 545.A, #0.1 ALA 252.B, #0.1 GLN 100.C Chain-final residues that are not actual C terminii: 606 hydrogen bonds Hydrogens added No SEQRES records for MD_polariz_ions22.pdb (#0.2) chain A; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.2) chain B; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.2) chain C; guessing terminii instead Chain-initial residues that are actual N terminii: #0.2 GLY 17.A, #0.2 GLN 1.B, #0.2 MET 1.C Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #0.2 THR 545.A, #0.2 ALA 252.B, #0.2 GLN 100.C Chain-final residues that are not actual C terminii: 621 hydrogen bonds Hydrogens added No SEQRES records for MD_polariz_ions22.pdb (#0.3) chain A; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.3) chain B; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.3) chain C; guessing terminii instead Chain-initial residues that are actual N terminii: #0.3 GLY 17.A, #0.3 GLN 1.B, #0.3 MET 1.C Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #0.3 THR 545.A, #0.3 ALA 252.B, #0.3 GLN 100.C Chain-final residues that are not actual C terminii: 605 hydrogen bonds Hydrogens added No SEQRES records for MD_polariz_ions22.pdb (#0.4) chain A; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.4) chain B; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.4) chain C; guessing terminii instead Chain-initial residues that are actual N terminii: #0.4 GLY 17.A, #0.4 GLN 1.B, #0.4 MET 1.C Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #0.4 THR 545.A, #0.4 ALA 252.B, #0.4 GLN 100.C Chain-final residues that are not actual C terminii: 646 hydrogen bonds Hydrogens added No SEQRES records for MD_polariz_ions22.pdb (#0.5) chain A; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.5) chain B; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.5) chain C; guessing terminii instead Chain-initial residues that are actual N terminii: #0.5 GLY 17.A, #0.5 GLN 1.B, #0.5 MET 1.C Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #0.5 THR 545.A, #0.5 ALA 252.B, #0.5 GLN 100.C Chain-final residues that are not actual C terminii: 620 hydrogen bonds Hydrogens added No SEQRES records for MD_polariz_ions22.pdb (#0.6) chain A; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.6) chain B; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.6) chain C; guessing terminii instead Chain-initial residues that are actual N terminii: #0.6 GLY 17.A, #0.6 GLN 1.B, #0.6 MET 1.C Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #0.6 THR 545.A, #0.6 ALA 252.B, #0.6 GLN 100.C Chain-final residues that are not actual C terminii: 584 hydrogen bonds Hydrogens added No SEQRES records for MD_polariz_ions22.pdb (#0.7) chain A; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.7) chain B; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.7) chain C; guessing terminii instead Chain-initial residues that are actual N terminii: #0.7 GLY 17.A, #0.7 GLN 1.B, #0.7 MET 1.C Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #0.7 THR 545.A, #0.7 ALA 252.B, #0.7 GLN 100.C Chain-final residues that are not actual C terminii: 615 hydrogen bonds Hydrogens added No SEQRES records for MD_polariz_ions22.pdb (#0.8) chain A; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.8) chain B; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.8) chain C; guessing terminii instead Chain-initial residues that are actual N terminii: #0.8 GLY 17.A, #0.8 GLN 1.B, #0.8 MET 1.C Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #0.8 THR 545.A, #0.8 ALA 252.B, #0.8 GLN 100.C Chain-final residues that are not actual C terminii: 595 hydrogen bonds Hydrogens added No MMTK name for atom "HA" in standard residue "LEU" No SEQRES records for MD_polariz_ions22.pdb (#0.1) chain A; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.1) chain B; guessing terminii instead No SEQRES records for MD_polariz_ions22.pdb (#0.1) chain C; guessing terminii instead Chain-initial residues that are actual N terminii: #0.1 GLY 17.A, #0.1 GLN 1.B, #0.1 MET 1.C Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #0.1 THR 545.A, #0.1 ALA 252.B, #0.1 GLN 100.C Chain-final residues that are not actual C terminii: 606 hydrogen bonds Hydrogens added Charge model: AMBER ff99bsc0 Assigning partial charges to residue CA (net charge +2) with am1-bcc method Assigning partial charges to residue MG (net charge +2) with am1-bcc method Assigning partial charges to residue CU (net charge +2) with am1-bcc method Non-standard atom names: GLN O2 (#0.1 GLN 100.C O2) ALA O1 (#0.1 ALA 252.B O1) GLN O1 (#0.1 GLN 100.C O1) ALA O2 (#0.1 ALA 252.B O2) THR O2 (#0.1 THR 545.A O2) THR O1 (#0.1 THR 545.A O1) Total charge for #0.1: 23.432 The following residues had non-integral charges: #0.1 THR 545.A 0.5679 #0.1 CYS 220.B -0.2719 #0.1 ALA 252.B 0.5679 #0.1 GLN 100.C 0.5679 Correct charges are unknown for 6 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 "O1" in standard residue "THR" 2016-06-29 13:19 GMT+02:00 James Starlight :

So the question is now related only to force-field optimization of the ensemble via Chimera. Assuming that I have several pdb snapshots consisted of protein in deffrent conformation (taken from the gromos force field after md done in gromacs) with the ions put to the binding pockets- now I need to make quick optimization of this ensemble. In my case just for the minimization using latest Amber ff aplied on those ensemble Chimera produced error related to assigning of the hydrogens (probably due to the mismatching between previous ff and amber however the same error in case if I remove all hydrogens prior to optimisation):

Args: () Traceback (innermost last): File "/opt/UCSF/Chimera64-1.11rc/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/opt/UCSF/Chimera64-1.11rc/share/chimera/baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "/opt/UCSF/Chimera64-1.11rc/share/chimera/baseDialog.py", line 704, in OK self.Apply() File "/opt/UCSF/Chimera64-1.11rc/share/AddH/gui.py", line 302, in Apply initiateAddHyd(self.molList.getvalue(), addFunc=method, okCB=self.cb, **kw) File "/opt/UCSF/Chimera64-1.11rc/share/AddH/unknownsGUI.py", line 274, in initiateAddHyd addFunc(models, **kw) File "/opt/UCSF/Chimera64-1.11rc/share/AddH/__init__.py", line 543, in hbondAddHydrogens inIsolation=inIsolation, **protSchemes) File "/opt/UCSF/Chimera64-1.11rc/share/AddH/__init__.py", line 554, in hbondAddHydrogens idatmType, hisNs, coordinations, inIsolation) File "/opt/UCSF/Chimera64-1.11rc/share/AddH/hbond.py", line 237, in addHydrogens hbonds = findHBonds(mlist, distSlop=recDistSlop, angleSlop=recAngleSlop) File "/opt/UCSF/Chimera64-1.11rc/share/FindHBond/base.py", line 574, in findHBonds (donorAtom, donorHyds) + args): TypeError: accPhiPsi() takes exactly 8 arguments (10 given)

TypeError: accPhiPsi() takes exactly 8 arguments (10 given)

File "/opt/UCSF/Chimera64-1.11rc/share/FindHBond/base.py", line 574, in findHBonds (donorAtom, donorHyds) + args):

Any alternative suggestions?

Gleb

2016-06-28 16:01 GMT+02:00 James Starlight :

...

Dear Pymol Users!

Within the Pymol session I have 2 loaded superimposed objects: 1) one experimental pdb consisted of protein with co-factors (ligand and metals); 2) ensemble of 20 MD snapshots of the same protein (superimposed on each others) without any cofactors;

For my particular task I need 1) to copy the selection (which include metals and ligand atoms) from the reference structure to each model of the MD ensemble (via Pymol), 2) make quick geometrical optimization of side-chains (I guess it better to do it using Chimera) within the active side of each model from MD ensemble 3) perform post-processing - analysis of the distances between cofactors and optimized side-chains of each MD conformers to obtain statistical distribution of averaged distances (I guess it better to do it via some MD software like Gromacs).

I will be very thankful for any suggestions for practical realization of those steps!

James

Hi Gleb, You should be reporting these via Help->Report A Bug rather than sending them to the entire chimera-users list. Please resubmit this using Report A Bug. —Eric Eric Pettersen UCSF Computer Graphics Lab

On Jun 29, 2016, at 4:19 AM, James Starlight wrote:

So the question is now related only to force-field optimization of the ensemble via Chimera. Assuming that I have several pdb snapshots consisted of protein in deffrent conformation (taken from the gromos force field after md done in gromacs) with the ions put to the binding pockets- now I need to make quick optimization of this ensemble. In my case just for the minimization using latest Amber ff aplied on those ensemble Chimera produced error related to assigning of the hydrogens (probably due to the mismatching between previous ff and amber however the same error in case if I remove all hydrogens prior to optimisation):

Args: () Traceback (innermost last): File "/opt/UCSF/Chimera64-1.11rc/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/opt/UCSF/Chimera64-1.11rc/share/chimera/baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "/opt/UCSF/Chimera64-1.11rc/share/chimera/baseDialog.py", line 704, in OK self.Apply() File "/opt/UCSF/Chimera64-1.11rc/share/AddH/gui.py", line 302, in Apply initiateAddHyd(self.molList.getvalue(), addFunc=method, okCB=self.cb, **kw) File "/opt/UCSF/Chimera64-1.11rc/share/AddH/unknownsGUI.py", line 274, in initiateAddHyd addFunc(models, **kw) File "/opt/UCSF/Chimera64-1.11rc/share/AddH/__init__.py", line 543, in hbondAddHydrogens inIsolation=inIsolation, **protSchemes) File "/opt/UCSF/Chimera64-1.11rc/share/AddH/__init__.py", line 554, in hbondAddHydrogens idatmType, hisNs, coordinations, inIsolation) File "/opt/UCSF/Chimera64-1.11rc/share/AddH/hbond.py", line 237, in addHydrogens hbonds = findHBonds(mlist, distSlop=recDistSlop, angleSlop=recAngleSlop) File "/opt/UCSF/Chimera64-1.11rc/share/FindHBond/base.py", line 574, in findHBonds (donorAtom, donorHyds) + args): TypeError: accPhiPsi() takes exactly 8 arguments (10 given)

TypeError: accPhiPsi() takes exactly 8 arguments (10 given)

File "/opt/UCSF/Chimera64-1.11rc/share/FindHBond/base.py", line 574, in findHBonds (donorAtom, donorHyds) + args):

Any alternative suggestions?

Gleb

2016-06-28 16:01 GMT+02:00 James Starlight :

...

Dear Pymol Users!

Within the Pymol session I have 2 loaded superimposed objects: 1) one experimental pdb consisted of protein with co-factors (ligand and metals); 2) ensemble of 20 MD snapshots of the same protein (superimposed on each others) without any cofactors;

For my particular task I need 1) to copy the selection (which include metals and ligand atoms) from the reference structure to each model of the MD ensemble (via Pymol), 2) make quick geometrical optimization of side-chains (I guess it better to do it using Chimera) within the active side of each model from MD ensemble 3) perform post-processing - analysis of the distances between cofactors and optimized side-chains of each MD conformers to obtain statistical distribution of averaged distances (I guess it better to do it via some MD software like Gromacs).

I will be very thankful for any suggestions for practical realization of those steps!

James

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