AMBER Archive (2006)

Subject: Re: AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" andthe RMS

From: Zhihong Yu (
Date: Mon Sep 25 2006 - 20:20:14 CDT

Dear professor Simmerling,

>your energies are very high- something must be wrong with your
>initial structure. we can't help with that since you didn't say how you
>built it.
    My complete system is a homodimer, the inhibitor existed between the interface. As you've mentioned in your JMC paper, I selected all residues within 20A of the inhibitor in the crystal structure to form my MD system, so there must be few separate short segments, can this result in wrong initial structure? I guess your system must be separate short segments too, did you treat with these segments with some special technique so as to it went on wheels?

    Moreover, as you've mentioned, I haven't add counterions to neutralize my MD system, so it has a charge of -9, could this result in very big "1-4 EEL" ?

>it could also be that your refc isn't the same as your inpcrd. we don't know since you didn't show the script.

    I've minimized added waters successfully (all solute fixed with 500 kcal/mol*A force constraints) to get a "relaxwater_min.rst" file, then in this step I used it as my "inpcrd" and "refc" file

    Thanks in advance, best regards!

    Zhihong, Yu

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