Re: [AMBER] Using WHAM to get 3D free energy surface in AMBER12

From: Wang Moye <>
Date: Tue, 17 Mar 2015 09:06:56 +0800 (GMT+08:00)

Thank you Jason!
I do the Temperature-REMD. Set 26 temperatures for the protein. Yes, as you said, the WHAM I mentioned is from Grossfield's lab. I don't use biased sampling. I saw the section 3 of the toturial. In that toturial the metafile contains the dihedral angle information through the script. I am confused with that I want to get wham-2D data and how to put the Rg and RMSD information into a metafile. After all, in the AMBER output files, there is no Rg and RMSD information clearly.
Thank you for your help!

Wang Moye

University of Chinese Academy of Sciences

> -----原始邮件-----
> 发件人: "Jason Swails" <>
> 发送时间: 2015年3月16日 星期一
> 收件人:
> 抄送:
> 主题: Re: [AMBER] Using WHAM to get 3D free energy surface in AMBER12
> On Mon, 2015-03-16 at 15:30 +0800, Wang Moye wrote:
> > Hello everyone!
> > I am a new user.There is a question in my objection and I need your
> > help. I run a REMD process in AMBER12.Now I obtain some output
> > files.Like this:
> > remd.mdcrd.001
> > remd.mdcrd.002
> > ...remd.mdcrd.026
> > and remd.mdinfo.001.. remd.mdinfo.026
> > and remd.rst.001.. remd.rst.002
> > and remd.mdout.001.. remd.mdout.026
> > Total 26 replicas. I want to get the 3D free energy surface picture
> > about my protein. Two coordinates are respectively Rg and RMSD.
> > Someone told me the WHAM code can do this. I have the WHAM code now,
> > but I don't know how to use the WHAM to deal with my AMBER's output
> > files to obtain the metafile. Should I write the Rg and RMSD
> > information into a single metafile? How to achieve this using the
> > outputfile above? Need I write some scripts to get the value of Rg
> > and RMSD?
> > If you know how to deal with it, please help me. Thank you very much!
> What kind of REMD did you do? Umbrella-REMD? Temperature-REMD?
> pH-REMD?
> Also, WHAM is a method, not a program. There are programs that
> implement WHAM, like the one from Grossfield's lab (I think that's the
> one you're talking about?)
> If you did not use biased sampling (like umbrella sampling), then you
> don't need a weighted histogram method -- just do unbiased histogramming
> and calculate your free energy from that.
> If you *did* do biased sampling, then there is an example constructing
> the WHAM metafile for Grossfield's program here:
> (specifically section
> 3:
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Mon Mar 16 2015 - 18:30:03 PDT
Custom Search