Thanks so much!
Indeed there are no any problems with ions in new AT !!
J,
2016-07-01 17:51 GMT+02:00 Pengfei Li <ambermailpengfei.gmail.com>:
> Hi James,
>
> AmberTools16 has nonbonded model parameter for various ions such as Mg2+, Ca2+, Cu+, Cu2+, Fe2+, Fe3+, and so on (just loading the leaprc.water.tip3p file if you are using TIP3P water model). If you want to use the bonded model for a specific metal ion, you can do the parameterization using MCPB.py.
>
> Kind regards,
> Pengfei
>
>> On Jul 1, 2016, at 4:37 AM, James Starlight <jmsstarlight.gmail.com> wrote:
>>
>> Thanks again!
>>
>> For sure in my case all ions should be coordinated because they are
>> embedded within the pockets of the protein. However just for the first
>> instance I would like just to build this model considering all ions as
>> non-bonding entries and then build the same considering coordinating
>> as well to compare local geomery of surrounded side chains! So,
>> assuming that I already have amber-tools-16 only for Cu ions some
>> special parametrization would be required, right?
>>
>> James
>>
>> 2016-06-30 18:20 GMT+02:00 Pengfei Li <ambermailpengfei.gmail.com>:
>>> Hi James,
>>>
>>> As Dave and Zoran suggested, you can load the leaprc.water.tip3p file if you are using TIP3P water. A nonbonded model could be good for Mg2+ and Ca2+ ions (the modeling is easy, just load the related learpc file as Dave and Zoran said). As for Cu and Fe ions, it depends on the problem you are trying to investigate. If there is no ligand switching or coordination number change, a bonded model would be better (MCPB.py is suggested to be used for the parameterization). Here is a tutorial about metal ion modeling in AMBER: http://ambermd.org/tutorials/advanced/tutorial20/ <http://ambermd.org/tutorials/advanced/tutorial20/>. Hope it helps.
>>>
>>> Kind regards,
>>> Pengfei
>>>
>>>> On Jun 30, 2016, at 9:05 AM, James Starlight <jmsstarlight.gmail.com> wrote:
>>>>
>>>> Thanks so much for the help!
>>>>
>>>> Yes defenetely the ions are coordinated with the protein - I will try
>>>> to switch to amber-tools 16 and report my progress after.
>>>>
>>>> Regards,
>>>>
>>>> James
>>>>
>>>> 2016-06-30 14:13 GMT+02:00 David A Case <david.case.rutgers.edu>:
>>>>> On Thu, Jun 30, 2016, James Starlight wrote:
>>>>>
>>>>>> source leaprc.ff03.r1
>>>>>> source leaprc.gaff
>>>>>
>>>>>> FATAL: Atom .R<CU 898>.A<CU 1> does not have a type.
>>>>>> FATAL: Atom .R<MG 899>.A<MG 1> does not have a type.
>>>>>> FATAL: Atom .R<CA 900>.A<CA 1> does not have a type.
>>>>>> FATAL: Atom .R<CU 901>.A<CU 1> does not have a type.
>>>>>> FATAL: Atom .R<CU 902>.A<CU 1> does not have a type.
>>>>>
>>>>> You are not loading any parameters for ions with charge greater than +1.
>>>>> You can look at the "Ions" section in the Reference manual for details
>>>>> about how to do this.
>>>>>
>>>>> I would strongly recommend upgrading to AmberTools16, since we have greatly
>>>>> simplified the handling of ions. Now, you choose a water model (say tip3p),
>>>>> and load leaprc.water.tip3p into tleap. This automatically loads the water
>>>>> parameters and corresponding monatomic ion parameters for a large number of
>>>>> ions. You can read about what is done in the "Ions" section of the new
>>>>> Reference Manual.
>>>>>
>>>>> ...dac
>>>>>
>>>>>
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Received on Mon Jul 04 2016 - 05:00:03 PDT
