RE: AMBER: Sander....

From: Ross Walker <>
Date: Tue, 3 Apr 2007 08:28:51 -0700

Dear Rita,

> After typing: $AMBERHOME/exe/sander -O -i -p
> -c ETOHBOX_init.rst -oETOHBOX_shake.rst -x
> ETOHBOX_shake.crd
> forrtl: severe (64): input conversion error, unit -5, file
> Internal Formatted Read

Do you really want to write the output to ETOHBOX_shake.rst? Typically one
would want to write the output to something like xxx.out. You would normally
specify xxx.rst as the restart file (which contains coordinates and
velocities). This is specified with -r.

So, here is my guess at what you did:

1) you started the first part of your simulation called and
instead of specifying -o ETOHBOX_init.out -r ETOHBOX_init.rst you specified
-o ETOHBOX_init.rst.

Thus if you look in ETOHBOX_init.rst I bet it contains the output data
rather than a set of coordinates and velocities.

2) You then provide this "output" file as the coordinates for the new run -c
ETOHBOX_init.rst and sander attempts to read it expecting a restart file but
instead gets a load of output data that it can't convert and so it quits.

My apologies if this is wrong but without seeing the actual files and the
command line you ran for the first section it is a little difficult to work
out exactly where the problem is.

Good luck,


|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Wed Apr 04 2007 - 06:07:45 PDT
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