To add to what Pengfei said here a little, you will need to write some
custom Python code in ParmEd to achieve what you want to do. The effect is
editing some elements of the LENNARD_JONES_BCOEF array in the topology
file, but you can use features of parmed to do it safely.
Then, as Pengfei said, use printLJMatrix to make sure you made the
modifications you intended. I will try to draft some sample code tonight
that will make the modifications you want to make.
HTH,
Jason
On Mon, May 9, 2016 at 10:23 AM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Dear Anu,
>
> For this situation, it seems you can not use ParmEd do that directly but
> you can user ParmEd to do it indirectly: you can use the “printLJMatrix”
> command in ParmEd to print out the A, B, Rmin, and epsilon values between Z
> atom type and other atom types, and you can manually modified these values
> to 0.00000000E+00 in the LENNARD_JONES_BCOEF region of the prmtop file (as
> long as these values are unique so you can determine their positions based
> on their values).
>
> Kind regards,
> Pengfei
>
> > On May 9, 2016, at 6:51 AM, anu chandra <anu80125.gmail.com> wrote:
> >
> > 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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> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
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> >>
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>
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--
Jason M. Swails
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Received on Mon May 09 2016 - 09:30:03 PDT
