Wow, that is great news to me.
thanks a lot.
Qiang
Berk Hess wrote:
Yes.
Gromos96 is the "inconvenient" force field in this respect (not OPLS).
In all other common biomolecular force fields you only need to change
the atom types, charges and masses.
Berk
> Date: Fri, 21 Nov 2008 18:01:15 +0800
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] OPLSAA parameters
>
> I mean in mutation free energy calculations.
>
> for OPLSAA force field we only need to provide the mutated atom types,
> but not need to change the [bonds], [angle] ...etc. in the topology
file?
> Since in Gromos96, the parameters need to be provided for state B.
>
> thank you
>
> Qiang
>
>
> Berk Hess wrote:
> > Hi,
> >
> > Although optionally having the parameters in the top file
> > might be useful, for mutation studies you don't need this,
> > since you only need to change the atom types,
> > you never have to give the parameters explicitly.
> >
> > Berk
> >
> > > Date: Fri, 21 Nov 2008 16:10:06 +0800
> > > From: [EMAIL PROTECTED]
> > > To: gmx-users@gromacs.org
> > > Subject: Re: [gmx-users] OPLSAA parameters
> > >
> > > Thanks Mark.
> > >
> > > Hope the developers can consider to output the parameters into .top
> > file
> > > explicitly. That would be helpful for mutation calculations at
least, I
> > > think.
> > >
> > >
> > >
> > >
> > > Mark Abraham wrote:
> > > > friendli wrote:
> > > >> Hi Mark,
> > > >>
> > > >> the atom types in .top file is opls_???, but the atom types(or
> > > >> "name") in [bondtypes] in ffoplsaabon.itp file is C, H, CT,
C_3, etc.
> > > >>
> > > >> So we still need to look up ffoplsaanb.itp to link these two
"atom
> > > >> type" (or "name"), right?
> > > >
> > > > OK, whatever... as I said, different force fields have different
> > > > mechanisms.
> > > >
> > > > Mark
> > > > _______________________________________________
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