Or generate the charmm topology in gromacs (expanded topology file via gmx
gromp -pp option) and run that through the parmed tool gromber. That's what
I do, but only because I am more familiar with gromacs than with charmm or
namd.
For that usage, single point energy evaluations between gromacs and amber
(both using charmm36 protein and lipid) are close but not exact. Though
note you need in this case to rename your water atoms or set the pmemd
inputs so that it knows how to settle the water properly.
On Tue, Feb 21, 2017 at 8:25 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Feb 21 2017 - 20:00:02 PST
