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

From: Fabian Glaser <>
Date: Wed, 20 Nov 2019 16:57:09 +0200

I tried with two additional different frames, same result, on exactly the same line…

| ERROR: I could not understand line 10006
   8.5142939 26.2329128 29.5113892

That is after I recenter the system, also without recentering I get an error, which is related I think

| ERROR: NaN(s) found in input coordinates.
           This likely means that something went wrong in the previous simulation.

Also to mention that in each stage of the US, I do min, equil and prod, and it’s only when I start the prod US that this error happens, the equil runs just fine, I can of course start the whole process again, but I would like to know what is wrong. Also I used cpptraj check but it does not produce any mistakes on the initial structure or on the equil structure.

I am probably missing something…. would it help if I send you more information? (input files etc)




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 20 Nov 2019, at 16:04, David A Case <> wrote:
> On Wed, Nov 20, 2019, Fabian Glaser wrote:
>>> cpptraj -p xxx.prmtop
>> trajin 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.
> It sounds like frame 92 in the trajectory file might be corrupt. Look at
> the "check" option in cpptraj, and the skipbadframes modifier. Dan may
> have better ideas on how to check the integrity of a netcdf trajectory
> file.
> But, the bottom line is that you may need to start from a different
> starting point.
> ....dac
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Received on Wed Nov 20 2019 - 07:00:02 PST
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