Hi Matthew,
Thanks,
I generated the files for tleap using the link you provided, so far MD is running but will evaluate how good the system behave later.
Best,
Zizhang
> On Jan 21, 2022, at 12:57 AM, Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu> wrote:
>
> Zizhang,
>
> It was a while ago that I worked on my project with ammonium sulfate. Looking back on the files, what I apparently did is follow the tutorial for parameterizing a non-standard residue <https://ambermd.org/tutorials/basic/tutorial4b/index.php <https://ambermd.org/tutorials/basic/tutorial4b/index.php>>(RESP charge fitting and assignment of GAFF atom types). You could improve on this by editing the frcmod or lib files to reflect literature values. I’ll send you all the files I used to construct the frcmod and lib files off-list just so you have the full story, but please give some thought to whether the GAFF parameterization is good enough or if you need to refine what I am going to share.
>
> Best,
> Matthew
>
>> On Jan 20, 2022, at 10:24 PM, zz sheng <shengzizhang.gmail.com <mailto:shengzizhang.gmail.com>> wrote:
>>
>> *Message sent from a system outside of UConn.*
>>
>>
>> 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> <mailto: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 Fri Jan 21 2022 - 06:00:02 PST
