AMBER Archive (2008)

Subject: Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)

From: Da-Wei Li (
Date: Mon Mar 24 2008 - 15:12:42 CDT

Do you use ASCII format? If it is, you can simple read the file by yourself.

I do not know exactly what happens but I fell there is sth wrong
associated with the file system(depend on the system you used). Pay
special care if your file size is large than 4G, in which case the 32
bit file pointer will meet overflow problem.


On Mon, Mar 24, 2008 at 3:01 PM, Qi Yan <> wrote:
> Hi,All:
> I got a trajectory file including 15000 frames and the file is 59G. When I
> try to strip Water and Ions, I got the following WARNING message:
> WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)...
> PTRAJ: Successfully read in 7917 sets and processed 7917 sets.
> Dumping accumulated results (if any)
> Does it mean that only number 7918 frame is corrupted? Can I simply ignore
> this frame? Actually, I don't know what is wrong with it. Does anybody can
> help me out?
> Thanks in advance,
> Qi
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