Hello Akshay,
Is your molecule is neutral or it has some charges? It
could be the problem with the molecule it self. My
suggession is to check the PDB file first, there may
be some wrong naming of the atoms in the file it self.
Are you getting some error message loading the pdb
file.
saurabh
--- Bill Ross <ross.cgl.ucsf.edu> wrote:
> > How can I neutralize the charge on my ligand which
> is not integral (it
> > is: 0.999960)? As you mentioned that Leap adds
> ions with integral
> > charge and thus the solute must have integral
> charge to arrive at 0. I
> > guess that is the reason TLEAP is not able to
> neutralize the decimal
> > charge on my ligand.
>
> Yes.
>
> > You also commented that "If you don't want to
> neutralize it with an
> > ion, I doubt it's a problem." >> Does this mean
> that I can simulate my
> > GPCR-Ligand-Membrane system using an overall net
> charge of 0.970410,
> > IS THIS ALLOWED, I MEAN, WILL THIS CHARGE NOT
> CREATE ANY ARTIFACTS
> > DURING MD SIMULATION?
>
> As a practical matter your biggest problem is
> probably not being able
> to neutralize rather than the non-integrality of the
> charge. Maybe Dave
> Case or Ross Walker can comment on the likely
> effects of running with a
> positive charge; I don't have experience in this.
>
> > If I have to neutralize this charge by making it
> an integer value of
> > 1, how can I do that for my ligand which otherwise
> has a charge of
> > 0.999960 ??
>
> You could revisit the charge derivation process and
> see what went
> wrong if anything. A simple hack would be to add
> .0001 to one atom,
> or even better to divide this among the atoms.
> Probably leap should
> be made to do this automatically for molecules that
> are within some
> small factor of integrality.
>
> Bill
>
> >
> > Thanks for your help and I look forward to hear
> from you.
> >
> > Best Regards
> >
> > Akshay Patny
> > The University of Mississippi
> >
> > -----Original Message-----
> > From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On
> > Behalf Of Bill Ross
> > Sent: Tuesday, January 23, 2007 11:30 AM
> > To: amber.scripps.edu
> > Subject: RE: AMBER: ADDIONS do not neutralize to
> ZERO
> >
> > > I have an organic ligand for which the charge is
> >>>
> > >
> > > > check TEL
> > > Checking 'TEL'....
> > > WARNING: The unperturbed charge of the unit:
> 0.999960 is not zero.
> > > Checking parameters for unit 'TEL'.
> > > Checking for bond parameters.
> > > Checking for angle parameters.
> > > check: Warnings: 1
> > > Unit is OK.
> > >
> > > Should this be a problem? I want to simulate the
> system with the
> > > organic ligand charged.
> >
> > I forget if there's a 'fudge factor' when
> neutralizing with ions.
> > This is pretty close to integral charge. If you
> can get it to 1.0
> > that could neutralize worry :-) If you don't want
> to neutralize it
> > with an ion, I doubt it's a problem. Otherwise try
> and see if it
> > gets neutralized.
> >
> > Bill
> >
> > >
> > > Thanks for help. Best Regards
> > > Akshay Patny (Olemiss)
> > >
> > > = = = = = = = = = = = = = = = = = = = = = = = =
> = = = = = =
> > > Akshay Patny
> > > PhD Candidate (5th Yr.), Computational Chemistry
> > > Department of Medicinal Chemistry, School of
> Pharmacy
> > > The University of Mississippi
> > > 805 College Hill Rd, # 9, Oxford, MS 38655
> > > E-mail: akshay17.olemiss.edu
> > > Phone (O): (662)-915-1286,(M): (662)-801-5496
> > > = = = = = = = = = = = = = = = = = = = = = = = =
> = = = = = =
> > >
> > > -----Original Message-----
> > > From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On
> > > Behalf Of Bill Ross
> > > Sent: Monday, January 22, 2007 7:58 PM
> > > To: amber.scripps.edu
> > > Subject: Re: AMBER: ADDIONS do not neutralize to
> ZERO
> > >
> > > >> addions2 ang Cl- 0
> > > > ERROR: The unperturbed charge of the unit:
> 0.970410 is not integral.
> > > > WARNING: The unperturbed charge of the unit:
> 0.970410 is not zero.
> > >
> > > > I defined in my command to neutralize the
> system until the charge
> > > > becomes '0'. Can you suggest me what is going
> wrong, or if it is
> > > > okay??
> > >
> > > If you were to 'check ang' before adding ions,
> the charge would
> > > presumably not be integral, e.g. .97041 after
> the decimal. Do you
> > > have any non-standard residues that might have a
> non-integral
> > > charge? Leap adds ions with integral charge and
> thus the solute
> > > must have integral charge to arrive at 0.
> > >
> > > Bill
> > >
>
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Received on Wed Jan 31 2007 - 06:07:16 PST
