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

From: kungking Hanpaibool <kunkungking.hotmail.com>
Date: Mon, 1 May 2017 15:59:59 +0000

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
> 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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--
-------------------------
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 ...
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Received on Mon May 01 2017 - 09:30:02 PDT
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