Re: [AMBER] DFTB3/MM simulations of CCCC zinc finger from Pengfei Li on 2019-03-28 (Amber Archive Mar 2019)

From: Pengfei Li <ambermailpengfei.gmail.com>
Date: Thu, 28 Mar 2019 12:09:44 -0400

Hi Ana,

You can try to use the QM/MM in AMBER with external QM program such as ORCA, Q-Chem, Gaussian, GAMESS-US, etc. Some of the QM programs are free of charge. You can check the section 10.2 in the AMBER 2018 manual: http://ambermd.org/doc12/Amber18.pdf <http://ambermd.org/doc12/Amber18.pdf>.

Hope it helps,
Pengfei

> On Mar 28, 2019, at 11:27 AM, Dreab, Ana <adreab.odu.edu> wrote:
>
> Hello Pengfei,
>
> Thank you for your reply. Actually, we plan to study a chemical reaction that involves the metal site, so we cannot run just MM simulation.
>
> Thank you again,
>
> Ana
>
> -----Original Message-----
> From: Pengfei Li <ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>>
> Sent: Saturday, March 23, 2019 3:36 PM
> To: AMBER Mailing List <amber.ambermd.org <mailto:amber.ambermd.org>>
> Subject: Re: [AMBER] DFTB3/MM simulations of CCCC zinc finger
>
> Hi Ana,
>
> I did not have this experience, but I know a similar example mentioned in the following reference "Lin, F.; Wang, R., Systematic derivation of AMBER force field parameters applicable to zinc-containing systems. J. Chem. Theory Comput. 2010, 6, 1852-1870.” Where the PM3/MM MD simulation gives a notable distortion of a zinc site.
>
> If you just want to simulate the vibration of the metal site (no chemical reactions), pure MM model is enough, you can try to use the zinc AMBER force field for your case: https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial20%2FZAFF.htm&data=02%7C01%7Cadreab%40odu.edu%7Ca9b1297d95f84e7407d508d6afc6f022%7C48bf86e811a24b8a8cb368d8be2227f3%7C0%7C0%7C636889666317187593&sdata=UusmKwHc55E%2F%2FIlPoye0ZOBg9RjOa1wkKCP2P6v4Gc4%3D&reserved=0 <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial20%2FZAFF.htm&data=02%7C01%7Cadreab%40odu.edu%7Ca9b1297d95f84e7407d508d6afc6f022%7C48bf86e811a24b8a8cb368d8be2227f3%7C0%7C0%7C636889666317187593&sdata=UusmKwHc55E%2F%2FIlPoye0ZOBg9RjOa1wkKCP2P6v4Gc4%3D&reserved=0> <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial20%2FZAFF.htm&data=02%7C01%7Cadreab%40odu.edu%7Ca9b1297d95f84e7407d508d6afc6f022%7C48bf86e811a24b8a8cb368d8be2227f3%7C0%7C0%7C636889666317187593&sdata=UusmKwHc55E%2F%2FIlPoye0ZOBg9RjOa1wkKCP2P6v4Gc4%3D&reserved=0 <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial20%2FZAFF.htm&data=02%7C01%7Cadreab%40odu.edu%7Ca9b1297d95f84e7407d508d6afc6f022%7C48bf86e811a24b8a8cb368d8be2227f3%7C0%7C0%7C636889666317187593&sdata=UusmKwHc55E%2F%2FIlPoye0ZOBg9RjOa1wkKCP2P6v4Gc4%3D&reserved=0>>, or use the MCPB.py to parameterize the metal site: https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial20%2Fmcpbpy.htm&data=02%7C01%7Cadreab%40odu.edu%7Ca9b1297d95f84e7407d508d6afc6f022%7C48bf86e811a24b8a8cb368d8be2227f3%7C0%7C0%7C636889666317187593&sdata=tVNJmn%2Fz3Mm9Kob8%2FQyhHiRrP0zGb8mZ2TCXrH5dCDM%3D&reserved=0 <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial20%2Fmcpbpy.htm&data=02%7C01%7Cadreab%40odu.edu%7Ca9b1297d95f84e7407d508d6afc6f022%7C48bf86e811a24b8a8cb368d8be2227f3%7C0%7C0%7C636889666317187593&sdata=tVNJmn%2Fz3Mm9Kob8%2FQyhHiRrP0zGb8mZ2TCXrH5dCDM%3D&reserved=0> <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial20%2Fmcpbpy.htm&data=02%7C01%7Cadreab%40odu.edu%7Ca9b1297d95f84e7407d508d6afc6f022%7C48bf86e811a24b8a8cb368d8be2227f3%7C0%7C0%7C636889666317187593&sdata=tVNJmn%2Fz3Mm9Kob8%2FQyhHiRrP0zGb8mZ2TCXrH5dCDM%3D&reserved=0 <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial20%2Fmcpbpy.htm&data=02%7C01%7Cadreab%40odu.edu%7Ca9b1297d95f84e7407d508d6afc6f022%7C48bf86e811a24b8a8cb368d8be2227f3%7C0%7C0%7C636889666317187593&sdata=tVNJmn%2Fz3Mm9Kob8%2FQyhHiRrP0zGb8mZ2TCXrH5dCDM%3D&reserved=0>>, https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial20%2Fmcpbpy_heme.htm&data=02%7C01%7Cadreab%40odu.edu%7Ca9b1297d95f84e7407d508d6afc6f022%7C48bf86e811a24b8a8cb368d8be2227f3%7C0%7C0%7C636889666317187593&sdata=xVIPJ4XCycciNPrBQfh4nylPbxPO0RmVVXDog6tjst0%3D&reserved=0 <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial20%2Fmcpbpy_heme.htm&data=02%7C01%7Cadreab%40odu.edu%7Ca9b1297d95f84e7407d508d6afc6f022%7C48bf86e811a24b8a8cb368d8be2227f3%7C0%7C0%7C636889666317187593&sdata=xVIPJ4XCycciNPrBQfh4nylPbxPO0RmVVXDog6tjst0%3D&reserved=0> <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial20%2Fmcpbpy_heme.htm&data=02%7C01%7Cadreab%40odu.edu%7Ca9b1297d95f84e7407d508d6afc6f022%7C48bf86e811a24b8a8cb368d8be2227f3%7C0%7C0%7C636889666317187593&sdata=xVIPJ4XCycciNPrBQfh4nylPbxPO0RmVVXDog6tjst0%3D&reserved=0 <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial20%2Fmcpbpy_heme.htm&data=02%7C01%7Cadreab%40odu.edu%7Ca9b1297d95f84e7407d508d6afc6f022%7C48bf86e811a24b8a8cb368d8be2227f3%7C0%7C0%7C636889666317187593&sdata=xVIPJ4XCycciNPrBQfh4nylPbxPO0RmVVXDog6tjst0%3D&reserved=0>>.
>
> Hope it helps,
> Pengfei
>
>> On Mar 21, 2019, at 12:18 PM, Dreab, Ana <adreab.odu.edu> wrote:
>>
>> Hi all,
>>
>> I am trying to run DFTB3/MM simulation (using Amber18) of CCCC zinc
>> finger and one of the cysteine residues keeps dissociating from the
>> Zn(II). Has anyone encounter a similar problem? Any help will be much
>> appreciated
>>
>> The qm region includes the Zn(II) and SCH2 fragment of each of the four cysteine residues. The overall charge of the qm region is -2.
>>
>> Best Regards,
>> Ana Dreab
>>
>> Department of Chemistry and Biochemistry Old Dominion University
>> Norfolk, VA 23529
>>
>>
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Received on Thu Mar 28 2019 - 09:30:03 PDT