Hi Chinthaka,
You can use that set for the bonded model. Since it is specified for 12-6-4 model, it would be
*better* for you to use the parameter sets specified for 12-6 model. The related information is in
the page 44 and 45 at Amber 14 manual.
http://ambermd.org/doc12/Amber14.pdf
You can check the related paper here:
http://pubs.acs.org/doi/abs/10.1021/ct400146w
My suggestion is using the CM or IOD parameter set for the VDW parameters in the bonded model.
HTH,
Pengfei
On Oct 20, 2014, at 2:28 PM, Chinthaka Ratnaweera <cnr88.msstate.edu> wrote:
> Ca parameters are there in the frcmod.ionslm_1264_tip3p in amber14
> developed by Li/Merz for TIP3P water (12-6-4 set).
> Can someone comment that this parameters are OK to use for bound Ca inside
> a protein?
>
>
> On Mon, Oct 20, 2014 at 12:57 PM, jinfeng liu <jinfengliu1119.gmail.com>
> wrote:
>
>> It is a free ion. Ok, I have read the amber manual for that. Thank you all.
>>
>> 2014-10-20 10:44 GMT-07:00 Jason Swails <jason.swails.gmail.com>:
>>
>>> On Mon, Oct 20, 2014 at 12:35 PM, jinfeng liu <jinfengliu1119.gmail.com>
>>> wrote:
>>>
>>>> Dear Amber users,
>>>>
>>>> I want to run MD simulation for a protein which contains a calcium. I
>>> know
>>>> the parameters of calcium are included in amber. So, what should I do
>> to
>>>> get amber know the calcium in the pdb. Thank you.
>>>>
>>>
>>> Please describe better what you are trying to do. Is it a bound
>> calcium?
>>> Do you want to model it using covalent bonds to various residues in your
>>> protein? Do you just want it as a free ion (if so, see chapter 3 section
>>> 9)? What have you tried so far? Did it not work? How did it fail?
>>>
>>>
>>> HTH,
>>> Jason
>>>
>>> --
>>> Jason M. Swails
>>> BioMaPS,
>>> Rutgers University
>>> Postdoctoral Researcher
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>>>
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>
>
>
> --
> Chinthaka Nadun Ratnaweera
> Hand Lab Rm 1126
> Department of Chemistry
> Box 9573
> Mississippi State University
> Mississippi State, MS 39762-9573
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Received on Mon Oct 20 2014 - 12:00:02 PDT
