Re: Re: AMBER: how can I deal with the puzzle?

From: ZhangJian <>
Date: Wed, 9 Mar 2005 15:59:42 +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

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Received on Wed Mar 09 2005 - 08:53:00 PST
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