The only way to use the CHARMM36 force field in Amber is to use either
CHARMM or NAMD to create a PSF file and then use the chamber action in
ParmEd to generate a prmtop and coordinate file compatible with Amber.
Alternatively, CHARMM-GUI creates an Amber topology file directly (it does
this by using ParmEd internally to do the conversion the same way I
suggested doing it above).
HTH,
Jason
On Tue, Feb 21, 2017 at 8:56 PM, Shanghaitech University WuMeng <
wumeng.shanghaitech.edu.cn> wrote:
> Hi,
>
> Thanks for your suggestions, Brian!
> I have read the ParmEd documentation. Then a new problem that confused me
> is with the help of ParmEd, does it means I need to generate a CHARMM
> system(maybe from the Charmm-gui) of CHARMM36 parameter set for the whole,
> or I just need to apply the CHARMM36 lipid force field to the membrane.
> If the former, can I use the prmtop file with CHARMM36 parameter set for
> the PMEMD directly; if the latter, how to realize it in Amber16(a mix of
> force fields ?).
>
> I am looking forward to receiving your reply. Thank you in advance!
>
> All the best,
> Wu Meng
>
>
>
> ------------------ 原始邮件 ------------------
> 发件人: "Brian Radak";<brian.radak.accts.gmail.com>;
> 发送时间: 2017年2月20日(星期一) 晚上11:55
> 收件人: "吴萌"<wumeng.shanghaitech.edu.cn>; "AMBER Mailing List"<
> amber.ambermd.org>;
>
> 主题: Re: Using CHARMM 36 force field in AMBER
>
>
>
> I strongly recommend copying additional emails like this to the listserv -
> archiving questions will help people with questions like this in the future.
>
>
> The most versatile and recent method for making force field modifications
> like this is the ParmEd program and library that is packaged with
> AmberTools. There is an updated CHAMBER equivalent therein:
>
> https://parmed.github.io/ParmEd/html/parmed.html#chamber
>
>
> I have not seen or done any specific tests to make sure that
> energies/forces are comparable between AMBER and other packages like CHARMM
> or NAMD when using files generated in this way.
>
> Ultimately, I expect the best way is to generate a CHARMM system in the
> usual way using something like CHARMM-GUI, although I'm not sure that this
> will automate the CHARMM36 inputs for AMBER (perhaps Jason or another
> ParmEd developer can comment on this?)
>
>
> HTH,
>
> Brian
>
>
> On Sat, Feb 18, 2017 at 9:32 PM, 吴萌 <wumeng.shanghaitech.edu.cn> wrote:
> Hi,
>
> Brian. You could see this e-mail because I searched on the Internet for
> using CHARMM 36 force field in AMBER and I read your e-mail in AMBER
> mailing list(http://archive.ambermd.org/201505/0427.html).
>
> I am worhing on a membrane protein sumulation in Amber, and I want to
> apply CHARMM 36 force field to the membrane. I have searched some methods
> such as using CHAMBER module in Amber, force switch in Amber16 and so on,
> but I am still confused about how to do it. So could you share me your
> experence on using CHARMM 36 force field in AMBER, more details is really
> welcomed.
>
> I am looking forward to receiving your reply. Thank you in advance!
>
> All the best,
> Wu Meng
> Shanghai, China
>
>
>
>
>
>
> --
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak.anl.gov
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
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Received on Tue Feb 21 2017 - 19:30:02 PST
