Dear Anselm, Matthew, and David,
Thanks very much for the suggestions. I attached the pdb file for the structure. I am not very sure if the SO4 should be there for MD but it appears in the structure and is very close to protein-protein interface.
The literature is very helpful.
Matthew, do you mind sending me the parameter files from the literature (.lib and .frcmod) for tleap? I truly have no idea how to generate them.
Best,
Zizhang
> On Jan 20, 2022, at 7:50 AM, Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu> wrote:
>
> Seconding Dr. Case’s points, you can check out Phys. Chem. Chem. Phys., 2017, 19, 20593.
> I think I used the parameters reported there when modeling the crystal structure of a protein with sulfates at the protein-protein interface.
>
> Best,
> Matthew
>
>
>
>> On Jan 20, 2022, at 7:05 AM, David A Case <david.case.rutgers.edu <mailto:david.case.rutgers.edu>> wrote:
>>
>> *Message sent from a system outside of UConn.*
>>
>>
>> On Thu, Jan 20, 2022, zz sheng wrote:
>>>
>>> My protein-protein interface has a SO4, I wonder how to parameterize it for
>>> MD? Could I use antechamber to generate the topology file and treat it as a
>>> 'ligand'? I saw ions have different ways of parameterization in the manual.
>>
>> First, are you sure the sulphate is present under the conditions you are
>> interested in? Unless you are simulating the crystal itself, that seems
>> unlikely.
>>
>> Second, yes, antechamber will give you a good starting point. One could try
>> to optimize those values based on experimental ion-water data. That is
>> unlikely to make a big difference, and the choice depends on how important
>> the sulphate is to your simulation.
>>
>> ....dac
>>
>>
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Received on Thu Jan 20 2022 - 19:30:02 PST
