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
------------------ ÔʼÓʼþ ------------------
·¢¼þÈË: "Brian Radak";<brian.radak.accts.gmail.com>;
·¢ËÍʱ¼ä: 2017Äê2ÔÂ20ÈÕ(ÐÇÆÚÒ») ÍíÉÏ11:55
ÊÕ¼þÈË: "ÎâÃÈ"<wumeng.shanghaitech.edu.cn>; "AMBER Mailing List"<amber.ambermd.org>;
Ö÷Ìâ: 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, ÎâÃÈ <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
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Received on Tue Feb 21 2017 - 18:00:02 PST
