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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>>
>>
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Received on Mon May 09 2016 - 07:30:05 PDT
