Hi Yuan,
(1) A topology file is needed for MD simulations using AMBER. Force field parameters are needed to build the topology file using LEaP. Even the QM part is dealt with QM software during the QM/MM simulation, force field parameters are still needed for building the topology file at the beginning.
(2) Meanwhile, MM equilibration is usually needed before QM/MM simulation, and during the MM equilibration force field parameters are necessary.
(3) Furthermore, during the QM/MM simulation, the VDW interactions between QM and MM parts are calculated based on Lennard-Jones parameters in the topology file.
Hope it clarifies.
Kind regards,
Pengfei
> On Nov 29, 2017, at 9:37 PM, MinYuan <minyuan.mail.ustc.edu.cn> wrote:
>
> Thank you for your kind help!
>
> Another question is,
> how about using QM/MM to study peptide and AsO3H3 interaction?
> I searched online and found others used ONIOM method to perform QM/MM calculations for AsO3H3 containing system.
>
> But the amber tutorials tell me, before QM/MM calculations, typing system force field is asked.
> I cannot understand,
> why still need to generate force field parameters for QM part, which mainly depends on QM software?
>
> Or did I miss anything important about qm/mm in amber?
>
>
> Looking forward to hear your reply.
>
> Best wishes
> Yuan Min
>> -----原始邮件-----
>> 发件人: "Andrew Schaub" <aschaub.uci.edu>
>> 发送时间: 2017-11-30 00:57:55 (星期四)
>> 收件人: "AMBER Mailing List" <amber.ambermd.org>
>> 抄送:
>> 主题: Re: [AMBER] how to generate the force fied file of AsO3H3?
>>
>> I posted on arsenic a couple of years ago:
>>
>> rom: Andrew Schaub
>> Date: Sat, 16 May 2015 22:55:13 -0700
>>
>> Another option for forcefield parametrization is the RED Server. I use
>> http://q4md-forcefieldtools.org/REDServer-Development/ . There is a
>> tutorial on how to use the server:
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
>> Francois on the RED mailing list just responded to someone also dealing
>> with arsenic parameter issues a few days ago. He suggested they look at
>> the following tutorial as a guide to parametrize arsenic using the RED
>> Server, http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo21.pdf
>>
>> On Wed, Nov 29, 2017 at 6:28 minyuan.mail.ustc.edu.cn <
>> minyuan.mail.ustc.edu.cn> wrote:
>>
>>> Thanks a lot！
>>> 1. http://pubs.acs.org/doi/pdf/10.1021/jp2051245 says that there is
>>> difference between As and P.
>>> It compares the two systems at QM level.
>>> Calculated interaction energies between As (P) and a water, As (P) and an
>>> alkali/ alkaline-earth metal cation.
>>>
>>> 2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337691/#notes-1 does
>>> force field modification via replacing As with P.
>>>
>>> However, it still remains unclear how to merge AsO3H3 parameters into
>>> force field file of peptide.
>>>
>>>
>>> Best wishes
>>> Yuan Min
>>>
>>>
>>> minyuan.mail.ustc.edu.cn
>>>
>>> From: David A Case
>>> Date: 2017-11-29 20:38
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] how to generate the force fied file of AsO3H3?
>>> On Wed, Nov 29, 2017, Bill Ross wrote:
>>>
>>>>> I want to put a small molecule (AsO3H3) into a peptide PDB file.
>>>> Maybe you can adapt GAFF params.
>>>
>>> GAFF only goes up to phosphorus.
>>>
>>> Don't forget that several companies offer free services that will search
>>> the internet to see what others have done in similar circumstances. I
>>> used google.com, and searched on "arsenious acid force field". The
>>> following looks like a useful starting point:
>>>
>>> www.ncbi.nlm.nih.gov/m/pubmed/21923105/
>>>
>>> ....dac
>>>
>>>
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Received on Wed Nov 29 2017 - 20:30:03 PST
