Hi Carlos,
Great! Best wishes for your research!
Warm regards,
Pengfei
> On Oct 30, 2015, at 3:06 PM, Carlos Modenutti <cpmode.gmail.com> wrote:
>
> Hi Pengfei,
> nobonded works very well.
> Thanks!
> Regards
> Carlos
>
> 2015-10-23 16:28 GMT-03:00 Pengfei Li <ambermailpengfei.gmail.com>:
>
>> Hi Carlos,
>>
>> Will you expect to see the ligand switching of the Ca2+ center? If not,
>> you can use the bonded model. If yes, (and also due to Ca2+ usually don’t
>> have much strong binding with the surrounding residues), I would recommend
>> you to use the nonbonded model or cationic dummy atom model. Amber has
>> nonbonded model parameters for Ca2+ available and the nonbonded model is
>> easier to set up than the cationic dummy atom model. So I would suggest you
>> try the nonbonded one first.
>>
>> Best,
>> Pengfei
>>
>>> On Oct 22, 2015, at 6:42 PM, Carlos Modenutti <cpmode.gmail.com> wrote:
>>>
>>> Dear Amber user group
>>> I need to carry out a molecular dynamics simulation of a protein
>>> carbohydrate complex but, in the carbohydrate binding site are two
>> calcium
>>> ions (in direct contact with ligand). Which is the better ion metal model
>>> for this situation? (bonded, nonbonded or cationic dummy atom model)
>>> Best regards
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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Received on Fri Oct 30 2015 - 13:00:03 PDT
