Re: [AMBER] Too many iterations in routine! in RMSD calculation

From: kungking Hanpaibool <kunkungking.hotmail.com>
Date: Mon, 1 May 2017 16:09:42 +0000

Hi Dan,


I also have another question.

Rmsd calculation for protein backbone, The result showed all of frame got 0.000.

Why didn't I got the result for backbone?


Best regards,

Kungking


________________________________
From: kungking Hanpaibool <kunkungking.hotmail.com>
Sent: Tuesday, May 2, 2017 12:59 AM
To: AMBER Mailing List; 'Daniel Roe'
Subject: Re: [AMBER] Too many iterations in routine! in RMSD calculation

ÁHi Dan,


I see, Thank you very much for your help.


Best regards,
Kungking

________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Tuesday, May 2, 2017 12:55 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Too many iterations in routine! in RMSD calculation

Hi,

Thanks for the log. Here is your problem:

```
  1: [rms reference :326 out ligand_100ns.rms]
    Target mask: [:326](1)
    Reference mask: [:326](1)
```

Residue 326 consists of 1 atom. You really need at least 3 atoms for
an RMSD to make sense (I probably should add a warning about this).

-Dan


On Mon, May 1, 2017 at 11:50 AM, kungking Hanpaibool
<kunkungking.hotmail.com> wrote:
>
> Hi Dan,
>
>
> The attached file is the cpptraj.out which was generated.
>
> Thank you for your help.
>
>
> Best wishes,
>
> Kungking
>
>
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Tuesday, May 2, 2017 12:29 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Too many iterations in routine! in RMSD calculation
>
> Hi,
>
> On Sat, Apr 29, 2017 at 5:16 AM, kungking Hanpaibool
> <kunkungking.hotmail.com> wrote:
> > When I saw the .log I found
> >
> > ----- 5lrnD_md49.nc (1-200, 1) -----
> > Too many iterations in routine!
> > Convergence failed.
>
> In my experience this either happens when not enough atoms are
> selected (so diagonalization of the covariance matrix fails) or you
> have corrupted coordinates. It would help to see the complete cpptraj
> log - can you send it to me off-list. Thanks,
>
> -Dan
>
> --
> -------------------------
> 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
The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
www.lobos.nih.gov
The Laboratory of Computational Biology is an interdisciplinary group of scientists who study biological processes via computer simulation. It is part of the ...



The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
www.lobos.nih.gov
The Laboratory of Computational Biology is an interdisciplinary group of scientists who study biological processes via computer simulation. It is part of the ...



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The Laboratory of Computational Biology<http://www.lobos.nih.gov/>
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The Laboratory of Computational Biology is an interdisciplinary group of scientists who study biological processes via computer simulation. It is part of the ...



> The Laboratory of Computational Biology
> www.lobos.nih.gov<http://www.lobos.nih.gov>
The Laboratory of Computational Biology<http://www.lobos.nih.gov/>
www.lobos.nih.gov
Website of the Laboratory of Computational Biology NHLBI NIH



The Laboratory of Computational Biology<http://www.lobos.nih.gov/>
The Laboratory of Computational Biology<http://www.lobos.nih.gov/>
www.lobos.nih.gov
Website of the Laboratory of Computational Biology NHLBI NIH



www.lobos.nih.gov<http://www.lobos.nih.gov>
The Laboratory of Computational Biology<http://www.lobos.nih.gov/>
www.lobos.nih.gov
Website of the Laboratory of Computational Biology NHLBI NIH



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--
-------------------------
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
The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
www.lobos.nih.gov
The Laboratory of Computational Biology is an interdisciplinary group of scientists who study biological processes via computer simulation. It is part of the ...
The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
The Laboratory of Computational Biology<https://www.lobos.nih.gov/lcb>
www.lobos.nih.gov
The Laboratory of Computational Biology is an interdisciplinary group of scientists who study biological processes via computer simulation. It is part of the ...
www.lobos.nih.gov<http://www.lobos.nih.gov>
The Laboratory of Computational Biology<http://www.lobos.nih.gov/>
www.lobos.nih.gov
Website of the Laboratory of Computational Biology NHLBI NIH
The Laboratory of Computational Biology is an interdisciplinary group of scientists who study biological processes via computer simulation. It is part of the ...
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Received on Mon May 01 2017 - 09:30:03 PDT
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