Hi,
You can check the tutorial online:
http://ambermd.org/tutorials/advanced/tutorial20/
HTH,
Pengfei
On Oct 20, 2014, at 3:09 PM, Chinthaka Ratnaweera <cnr88.msstate.edu> wrote:
> We previously followed http://archive.ambermd.org/200709/0211.html to make
> a library file. Still this is a nonbonded model. However in long run
> Calcium's were not stable. Can you please send the details or a link to
> create bonded parameters.
>
> On Mon, Oct 20, 2014 at 1:50 PM, Ken Merz <kmerz1.gmail.com> wrote:
>
>> 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
>>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
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>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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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>>
>
>
>
> --
> 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 - 14:30:03 PDT
