AMBER: For further question about Targeted MD

From: ZhangJian <>
Date: Wed, 9 Mar 2005 20:48:44 +0800

Thomas E. Cheatham, Hi.

    Thank you for your reply on TMD. I am a new one for amber, I think I should better say more detail about my project, could you give me a suggestion?
    Now I have two conformation of a protein. I choosed one as initial conformation, added WATER216 within box(10.0 angstroms), minimized and increased temperature from 0K to 300K.
I put another conformation into the xleap for adding the same number of WATER216, and used it as a ref. RMSD between two conformations measured by spdbv is below 14 angstroms, but when I run the sander using parameters that I provided last time, it showed above 440 angstroms(maybe water was calculated, I don't know about it), thought I refined the group that only consist of protein atom in the parameter file.
    I have seen some targeted MD examples provied in tgtmd directory, but I don't know that when I use the implicit solvent, How can I deal with explicit solvent that I added during the minimization and the process of increasing temperature(Should I delete them? or only perform minimization and increasing temperature without water?) Could you give me some tips of reasonable GB parameters with other conditions (PME and cutoff)?

        I used 10000 step in order to test change on RMSD only from 442 to 440, it is not complete time for whole change, and dt=0.0005 is a sample from examples(I thought 0.002 may be suitable enough). I want to give more accurate non-bond interaction using larger cutoff.

        I am suffering about this and very appreciated for you help. Thank you in advance


> I have two conformations of a protein which have a RMSD of 440
> angstrom. I want to transfor from one conformation to another. In the

>Are you sure that the difference is 440 angstroms or 44 nm? If so this is
>of such an extremely large size that a few picoseconds (10000 * 0.0005 or
>5 ps) will not be sufficient to move the system at all. It is very
>unlikely that the system can adapt to such large force/structure changes
>(on the order of 400 angstroms) in such a short period of time.

> imin=0, nstlim=10000, dt=0.0005,

>Why do you need to have the timestep so short (using SHAKE); are their
>instabilities in the system to begin with?

> ntpr=10, scee=1.2, cut=25,
> igb=0, irest=1, nmropt=1,

>It appears that you are not using generalized Born (implicit solvent) yet
>you have a large cutoff and PME was not turned off (in the &ewald namelist
>setting use_pme=0 ?); this is a bit confusing. Do you want gas phase?

> itgtmd=1, tgtrmsd=0.0, tgtmdfrc=0.5,
> &end
> &wt
> TYPE='TGTRMSD', istep1 =1, istep2 = 1000,
> value1 = 441.2, value2 = 440.,
> &end

>400 angstroms is a really large number in the atomistic world of AMBER

> 2.And In the output file, I found the temperature increased from 300K to
> 320K during 10000 steps, the whole energy was increased from negative
> value to positive. is it right? 3.Should I use the Born model(igb=1) for
> targeted MD?

>Do you have solvent? If not, figure out carefully how to run a vacuum
>simulation. If you can afford it, run GB (or implicit solvent) and even
>better explicit solvent (which can be debated); however the size system
>you are investigating (if the 400 angstroms RMSd is correct) is really at
>the cutting edge of what is currently possible.

>To better your understanding of targeted MD and these simulation
>protocols, it may be advantageous to run a small system first to test
>things out; watch movies, plot the energies and values and see what is

Feel free to ask the list for further advice as many, if they understand
your problem well, will provide excellent insight beyond my comments.

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Received on Wed Mar 09 2005 - 13:53:00 PST
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