Re: [AMBER] problem during MD process

From: 蒋峻峰 <asakiayumikio.gmail.com>
Date: Mon, 13 Dec 2010 00:06:41 -0800 (PST)

dear case!

What i am concerning is that if i do not fix the atoms, the distance between NZ of lysine and C of ACO will be larger than 5 Ang.While in acetylation process, this must be wrong. Thus i am eager to know how does it happen, is that the problem of initial complex structure or any ohter related problems. If you do know the key to solve this problem, please tell me, thank you.

        2010-12-13
        J.F. Jiang
        asakiayumikio.gmail.com





发件人:case
发送日期:2010-12-13 11:53
收件人:AMBER Mailing List
抄送:
主题: Re: [AMBER] problem during MD process
On Sun, Dec 12, 2010, 蒋峻峰 wrote: > I am doing a project of acetyltransfer of ACO. > > Stilly, the rmsd of the whole structure turned larger than 2 > after 4ns simulation. You don't say how large the structure is, or what atoms you used to compute the rms difference. A 2 Ang. RMS change is not at all unusual, especially for a sizeable protein, or if you are looking at all atoms. Also, if there are floppy N- or C-terminal residues (or some floppy loop) they can have a big effect on the computed RMS. The best thing to do is to carefully examine the trajectory in a viewer like Chimera or VMD. Don't concentrate on just a single number, but look to see what is happening, both at the active site, and to the protein as a whole. Start with seeing if the secondary struture is conserved, then look at more details. ...good luck...dac _______________________________________________ AMBER mailing list AMBER@ambermd.org http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Dec 13 2010 - 00:30:02 PST
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