Yes, you can also use this one: frcmod.ionslrcm_cm_tip3p (or spce or tip4pew, depends on
the water model you are using).
HTH,
Pengfei
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
>>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
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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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>>
>
>
>
> --
> 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 - 12:00:03 PDT
