Re: [AMBER] Simulating a periodic System about Molecular Crystal

From: hanlu0366 <>
Date: Mon, 6 Jun 2011 11:34:12 +0800

Dear sir:

In my process , I did follow the Tutorial A13,but I come across another problem that the software let you to set a box when you set ntb = 1 . I want to ask whether the tools which is used to establish the Crystal in AmberTools 1.5 make the structure established containing the periodic boudary conditions . If they make the structure estabished containing periodic boundary conditions ,why the software ask for your setting box (ntb=1).

                                                                                                                                                Yours Sincerely




发件人: case
发送时间: 2011-06-05 22:26:49
收件人: AMBER Mailing List
主题: Re: [AMBER] Simulating a periodic System about Molecular Crystal
On Sun, Jun 05, 2011, hanlu0366 wrote:
> I am simulating a Molecular Crystal by AmberTools 1.5 & Amber 11. I
> established a pdb of supercell sucessfully by methods in Amber turials
Have you tried to follow Tutorial A13? That should help a lot in setting up
crystal simulations. You would ordinarily *not* use setBox in LEaP, but the
more specialized preparation tools listed there.
...good luck....dac
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