On Jun 29, 2016, at 4:19 AM, James Starlight <jmsstarlight@gmail.com> 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 <jmsstarlight@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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