Hi,
Thank you for your reply!
I am so sorry that I can not understand your meaning completely. In my opinion, you hope me calculate the distance between different NO3- and metal ion for imaged structure. Then how can I make sure how many NO3- coordinate with metal ion for imaged structure? If there are two NO3 coordinated with metal ion, is NO3 with largest distance the third one?
I hope to use this structure to do QM/MM calculation, so I need to know the true structure.
With my best regards,
Junbo
> -----原始邮件-----
> 发件人: "Daniel Roe" <daniel.r.roe.gmail.com>
> 发送时间: 2017-05-04 23:49:53 (星期四)
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 抄送:
> 主题: Re: [AMBER] The problem for image tool in AMBER
>
> Hi,
>
> First, 'autoimage' is usually a better command for re-imaging your trajectory.
>
> Second, when you have periodic boundary conditions you have to think
> in terms of cell periodicity. For example, if in your first structure
> (with apparently only 2 NO3- coordinating with your metal) the metal
> ion is near a unit cell boundary, you could have a third NO3- nearby
> that has been translated due to imaging. If after imaging you have 3
> NO3- near the metal, this is probably what happened. You can also
> calculate the distance of each NO3- to the metal to verify - the
> 'distance' command will use the minimum imaged distance.
>
> -Dan
>
>
> On Wed, May 3, 2017 at 11:20 PM, 鲁俊波 <lujb15.mails.tsinghua.edu.cn> wrote:
> > Dear all:
> > I have done a molecular dynamics. But I encounter a problem when I see the structure. The attached file am_cro_md.rst is my last structure of molecular dynamics trajectory, and md.in and am_cro.prmtop are the control and top files. I convert the structure to the pdb file using cpptraj:
> > trajin am_cro_md.rst
> > trajout am_cro_md1.pdb
> > This structure seems no periodic. So I use the image tool:
> > trajin am_cro_md.rst
> > image center
> > trajout am_cro_md2.pdb
> > This two structures are different. The metal ion coordinates with two NO3- for first structure, but with three NO3- for second structure.They are so strange. I want to choose some solvent to do QM/MM optimization. So I do not know choose which structure. Is there something wrong? Can anyone give me a help?
> > With my best regards,
> > Junbo
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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Received on Thu May 04 2017 - 10:00:02 PDT
