Re: [AMBER] ambpdb error

From: Jason Swails <>
Date: Tue, 19 Aug 2014 08:04:03 -0400

On Tue, 2014-08-19 at 13:12 +0200, Urszula Uciechowska wrote:
> My mistake, I am using *.rst file
> ambpdb -p *.prmtop <*.rst> *.pdb

If you are using this command *exactly*, it's unlikely to be doing what
you want it to do. The wildcard expansion that the shell usually does
will expand *.prmtop into a list of all files that end in .prmtop, and
the same with *.rst and *.pdb. If no files match, then it will simply
use the file name with the * still in it.

However, the error message you got says:
forrtl: severe (64): input conversion error, unit 5, file stdin

What this means is that the program could not convert one of the fields
it tried parsing from standard input into the correct type. Since the <
character tells the shell to print a file to a program's standard input,
that means that somewhere in the *.rst file there is a substring that
ambpdb cannot convert to a floating point number. It could be that
there is a set of *****'s indicating atoms have overflowed. It could be
that your *.rst file is a NetCDF restart if you're using ntxo=2 in your
sander/pmemd input file. It could be that your shell is picking up the
"wrong" .rst file if you're really using *.rst. It could be that you
accidentally wrote the trajectory file with the extension .rst. The
fact is that only you (who actually has the files) can figure out
exactly what went wrong.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Aug 19 2014 - 05:30:02 PDT
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