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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> >>
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Received on Thu Aug 18 2016 - 12:30:02 PDT
