Hi,
You could use the parameter sets mentioned by Pengfei, but you might want to try the nonbonded model first. It might work fine without needing to create the bonded parameters, etc. Worth a quick test. Kennie
> On Oct 20, 2014, at 2:47 PM, Chinthaka Ratnaweera <cnr88.msstate.edu> wrote:
>
> So is this the one you recommend frcmod.ionslrcm_iod? Or one with the TIP3P?
> Thanks
>
>
> On Mon, Oct 20, 2014 at 1:38 PM, Pengfei Li <ambermailpengfei.gmail.com>
> wrote:
>
>> 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
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
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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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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
>
>
> --
> Chinthaka Nadun Ratnaweera
> Hand Lab Rm 1126
> Department of Chemistry
> Box 9573
> Mississippi State University
> Mississippi State, MS 39762-9573
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Oct 20 2014 - 12:00:04 PDT
