Hi Raghuvir,
I agree with Jason's advice. From your description, I think there may be
the problem with different naming schemes or lib files for the ions:
In ff14SB I think there will the AMBER default values:
Zn 1.1 0.0125
While in opls_parm.dat file, there is:
ZN 1.85 0.06
So here they used different atom types: one is Zn and the other is ZN.
I am not sure which kind of library file for ions ff14SB force field using. If that library doesn't contain the
the Zn ion, AMBER will not recognize the Zn ion automatically, you need to set the atom type and
charge for it manually in the tleap.
If you like you can attach the pdb file and input file of leap. I can help you to check it out.
Pengfei
On Mar 27, 2014, at 12:16 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, 2014-03-27 at 21:16 +0530, R R S Pissurlenkar wrote:
>> Hello
>>
>> I tried loading pdb with Zn atom using ff14SB force field. However I
>> get error message as regards to van der waals parameters. Also I
>> noticed that the parameters for ZN are mentioned in opls_parm.dat
>> file. How do I use them
>>
>> Please help me
>
> Without knowing exactly what you did or exactly what error messages you
> got, we cannot help.
>
> Your description or interpretation of what was done or printed does not
> help us understand what happened.
>
> HTH,
> Jason
>
> I would also suggest putting the error message you got into a google
> search and see if the problem was seen before. If your question has
> already been answered, it will save everybody time by taking advantage
> of the existing archives.
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Thu Mar 27 2014 - 16:00:02 PDT
