Re: [AMBER] RROR: I could not understand line - during US

From: Fabian Glaser <>
Date: Wed, 20 Nov 2019 13:44:35 +0200

Dear David,

Thanks a lot for your help, here are the answers to your questions,

First, I would like to mention that this is a repetition of a previous successful attempt to perform US. The original one started form the x-crystal structure of the protein + ligand (heme + Fe) and went perfectly ok. This one started from a specific frame extracted from a long MD, so I am expecting some structural changes. Does that something to do with this error?

The program is indeed stopping while trying to read the previous rst7 file, which in this case is a centered equilibrated previous stage (as I am trying to do equil + prod for many ligand-protein distances). Additionally, the MD runs for 2ns and only then when I try to restart again it dies… weird. I know the rst7 of course, and when looking at the 10006 line is lacking part of it, here it is with +3 and -3 lines around it:

  33.7215987 41.1201582 50.2499269 55.4859958 21.3058916 22.8424992
  55.9790454 20.8244135 23.5068128 54.8608843 21.8311679 23.3420514
  15.9153426 3.3317946 18.6221599 15.4269558 4.0174390 19.0777934
  16.6825041 3.1775361 19.1734306
   0.1788098 -0.2230289 0.3519713 0.9994690 -0.7597210 -0.1893879
   0.1944981 -0.3642163 0.4440787 -0.3630756 -0.1984616 -0.0881926
   0.2481594 -0.0561125 -0.0508682 -0.3048515 -0.0445942 0.2342675

The bolded line is 10006, so is missing the las three numbes, correct? And yes the file is the same size of other rst7 files. I also tried a short simulation without the nmrtop = 0 and still the same problem occurs. I have no idea where to look.




Fabian Glaser PhD

Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Tel +972 (0) 4 8293701

> On 19 Nov 2019, at 22:41, David Case <> wrote:
> On Tue, Nov 19, 2019, Fabian Glaser wrote:
>> I got the following error in a more prod.2.4.out file, during a umbrella
>> sampling, so this is just one of the stages, and looking at the last rst7
>> file I see there is an incomplete line, but I cannot understand what is
>> the reason or why is that. I repeated the simulation several times with
>> different conditions, allwasy the same result.
>> | ERROR: I could not understand line 10006
>> 3.9479593 29.5242775 24.6576289
> It's a little hard to follow your report. What is a "more prod.2.4.out"
> file? It mostly looks like the program is having trouble reading an
> rst7 (restart) file, and this might have nothing to do with umbrella
> sampling.
> Do you know which file is being read when the error appears? Can you
> look at lines around 10006 in that file? What do you see? Is this file
> the same length as other rst7 files you have for this system?
> If you run a short simulation with and without umbrella sampling, does
> the error above appear with umbrella sampling and go away without it?
> Basically, we need to know more about what is going on here.
> ...dac
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Received on Wed Nov 20 2019 - 04:00:02 PST
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