Thanks Bill,
I looked to your suggestion and I found that the are many values replaced with ’-nan’, I guess this is not good. I did not find values like this in any of the previous rst7 files….
I also recall now that I extracted the initial rst7 file for this run from a production md, using the following cpptraj commands, which produces ASCII file… is that the source of the problem?
>cpptraj -p xxx.prmtop
trajin xxx.nc 92 92
trajout md1.554.rst7 restart
go
This md1.554.rst7 was the one I used to start teh simulation, and I noticed also that wehn I run this again with a different frame from the same file md1.554.rst7, it seems to work fine…. So I am really puzzled.
Thanks!
Best,
Fabian
Fabian Glaser PhD
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web
http://bku.technion.ac.il/
Tel +972 (0) 4 8293701
> On 20 Nov 2019, at 13:50, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> What if the last atom's xyz was on the line w/ 3 numbers, then the
> velocity vectors start on a new line?
>
> Bill
>
> On 11/20/19 3:44 AM, Fabian Glaser wrote:
>> 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.
>>
>> Thanks!
>>
>> Best,
>>
>> Fabian
>>
>> Fabian Glaser PhD
>>
>> Bioinformatics Knowledge Unit - BKU
>> The Lorry I. Lokey Center for Life Sciences and Engineering
>> Technion - Israel Institute of Technology, Haifa, Israel
>> Web http://bku.technion.ac.il/
>> Tel +972 (0) 4 8293701
>>
>>> On 19 Nov 2019, at 22:41, David Case <david.case.rutgers.edu> 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 - 05:30:02 PST
