Dear Pengfei,
Many thanks for the reply. Unfortunately, most of the ParmEd commands
require epsilon and Rmin/2 as input. In my case, B coefficient of Z atom
type is zero as it is calculated using Bi = Bii^1/2. All I want to do is
here that to change LENNARD_JONES_BCOEF values in parmtop to zero for those
combinations where Z atom type is involved and I wonder whether the ParmEd
can do it.
Many thanks
Anu
On Sun, May 8, 2016 at 3:55 AM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Dear Anu,
>
> There are some commands in ParmEd about modifying the LJ parameters: e.g.
> “changeLJPair”, “changeLJSingleType”, and “addLJType” (you can check the
> AMBER manual for details). They may be helpful for your work.
>
> Kind regards,
> Pengfei
>
> > On May 7, 2016, at 11:52 AM, anu chandra <anu80125.gmail.com> wrote:
> >
> > Dear Amber users,
> >
> > I am trying to use a modified parameter set from the literature for
> > simulation, where the B coefficient of LJ potential the one atom type (
> for
> > e.g. atom type Z) is set as zero. In oder to implement this the amber
> > topology, I have to modify the LENNARD_JONES_BCOEF values to zero for
> each
> > pair of atom type, where atom type D in involved in the pair. Is there an
> > build script in Amber that can help me to do such modification in the
> > topology file?
> >
> >
> > Many thanks in advance
> >
> > Anu
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>
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Received on Mon May 09 2016 - 04:00:04 PDT
