Hi!
I tried
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm.
Apart from "Error: Atom XXX was assigned a lower molecule # than
previous atom" error, which was fixed as described, all is good there.
Still there was error in minimization.
I am trying restrained non bonded model. Will post success or failure.
Thanks for the advice.
On Fri, Aug 19, 2016 at 6:48 AM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Abhilash,
>
> You can use the checking method shown in the MCPB.py tutorial:
> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <
> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>. If there is
> nothing wrong with the parameters, it should be because there is only
> partial charge but no VDW parameters in the water hydrogen, in which
> situation you can use a restrained nonbonded model or a hybrid model
> (restrained nonboned model for the two waters + bonded model for the other
> metal ligating residues) to the simulation, as described in the end of the
> MCPB.py tutorial.
>
> Kind regards,
> Pengfei
>
> > On Aug 18, 2016, at 3:17 PM, Abhilash J <md.scfbio.gmail.com> wrote:
> >
> > Hi!
> >
> > I tried and was successful in creating prmtop and inpcrd files. Thanks
> > for the help. Gaussian was the only time taking step.
> > But i am still unable to run the simulation.
> > My system has 2 water molecules, a ligand and 1 residue (ASN) in
> > co-ordinate bond with an ion.
> > The problem is the water molecules come in clash with ASN during
> > minimization. I tried different geometries (small changes) all in vain.
> > I know it is the right starting geometry as it is reported in crystal
> > structure.
> > Please advice.
> >
> >
> >
> > On Tue, Aug 16, 2016 at 8:10 PM, Pengfei Li <ambermailpengfei.gmail.com>
> > wrote:
> >
> >> Hi Abhilash,
> >>
> >> Since it is a homo dimmer, you can parameterize a monomer and use the
> >> generated parameters for both monomers. You can treat the two active
> site
> >> with the same parameter set, in which way you need to manually rename
> the
> >> active site residues on the other monomer (other than the one used for
> >> parameterization) according to the new residue names MCPB.py generated
> for
> >> the active site residues of the monomer you have parameterized. Also you
> >> need to mirror the related commands “e.g. bond commands” in the tleap
> input
> >> for the other monomer.
> >>
> >> You can also prepare the two monomer system separately and finally use
> the
> >> combine command to combine them (like sunita said).
> >>
> >> Kind regards,
> >> Pengfei
> >>
> >>> On Aug 12, 2016, at 3:50 PM, sunita guptacDgug <sunita.bio.gmail.com>
> >> wrote:
> >>>
> >>> Yes...in tleap we can combine many molecules together to make a
> complex.
> >>> Eg. Load protein as x variable..1st ligand as y and 2nd ligand as z.
> >> Later
> >>> combine x y z as another variable and save it as complex.top and
> >> complex.crd
> >>>
> >>> Hope it helps you
> >>>
> >>> On 12-Aug-2016 10:42 PM, "Abhilash J" <md.scfbio.gmail.com> wrote:
> >>>
> >>>> Hi everyone!
> >>>>
> >>>> I need to prepare a homo dimer system with each monomer having a
> >> ligand
> >>>> and a metal ion in its active site.
> >>>> Both active sites are far from each other and don't affect each other
> >>>> directly.
> >>>> I think I will be able to prepare the one active site at a time using
> >>>> mcpb.py tutorial. (I have gone through the tutorial)
> >>>> How is it possible to prepare the complete complex (2 monomers with
> >>>> their respective ions and ligands) together?
> >>>> Is it possible to prepare the system one active site at a time and
> >> join
> >>>> them together to complete the system.
> >>>> Please advice.
> >>>>
> >>>>
> >>>>
> >>>> Regards
> >>>> _______________________________________________
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> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
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> >>
> >>
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Received on Thu Aug 18 2016 - 21:30:07 PDT
