[Chimera-users] Transfer of the selection from reference to the ensemble

Eric Pettersen pett at cgl.ucsf.edu
Wed Jun 29 10:14:28 PDT 2016


Hi Gleb,
	Same here.  Please resubmit via Report A Bug.

—Eric

> On Jun 29, 2016, at 8:31 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> 
> 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 <jmsstarlight at gmail.com>:
>> 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 <jmsstarlight at gmail.com>:
>>> 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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