ok, you are right.
Thank you Jacopo for the elucidation.
Stefania
2016-10-06 15:53 GMT+02:00 Jacopo Sgrignani <sgrigna.gmail.com>:
> Dear Stefania
> I had a look to the 1991 paper and as I remembered it is a bonded model
> (i.e. you have covalent bond between ligands and the metal ion).
> The 2014 paper seems to be a non-bonded model.
> In my experience non-bonded models usually do not rigidly conserve the
> coordination over the simulation.
>
> regards
>
> Jacopo
>
>
> 2016-10-06 15:34 GMT+02:00 Stefania Mirabella <stefania.mirabella.unifi.it>:
>
>> Hi!
>> I am Stefania and I would like to ask your help. I am using Amber 12
>> to perform a MD of a complex of a ligand with a metalloprotein,
>> containing Zn.
>> This Zn is coordinated to two Histidine residues (HID) in all the
>> reported X-ray crystallogrphic studies and in all the reported
>> dynamics with this protein, so I would like to mantain this kind of
>> coordination during my dynamics.
>> Initially, I tried with the zinc frcmod file with the older parameters
>> published by Merz in 1991 for TIP3P water solvatation (JACS 1991, 113,
>> 8262)
>> Zn2+ 1.100 0.0125000
>> and in this case the coordination with histidines was kept, as it
>> seems more reasonable.
>> Then, I found out the newer Zn parameters reported by Merz in 2014
>> (JCTC 2014, 10, 289)
>> Zn2+ 1.455 0.02662782
>> In this case the coordination of the Zinc changes a lot during the
>> dynamics, loosing the coordination of one Histidine and also of my
>> ligand.
>> So, it seems less reasonable if compared with other dynamics performed
>> with similar ligand.
>> What do you think it could be the problem? What is the difference
>> between the two sets of VdW parameters?
>>
>> P.s. the protonation of Histidines was the same for both the performed
>> dynamics.
>>
>> Thank you very much!
>> My best regards,
>> Stefania
>>
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Received on Thu Oct 13 2016 - 06:00:03 PDT
