Re: AMBER: imin=5 in sander

From: Carlos Simmerling <>
Date: Mon, 06 Dec 2004 20:52:14 -0500

you didn't specify the trajectory using the -x flag.
-c and -ref should still be input coordinates, not
trajectory. -ref is only needed if you are using positional
or RMSD restraints.

look at tests/trajene for an example.



>Hi Amber users,
>I am trying to run sunder with imin=5 parameter for trajectory analysis. But
>sander cannot process my trajectory file. Sander reads rst or inpcrd files but
>gives out this message when I try to run with a mdcrd file:
>fmt: read unexpected character
>apparent state: internal I/O
>last format: (i6,e15.7)
>lately reading sequential formatted internal IO
>./min5_EN.q: line 7: 15353 Aborted $AMBERHOME/exe/sander -O -i
> -o min5_EN.out -p 3_20.prmtop
>-c 3_20.mdcrd -r new.rst -ref 3_20.mdcrd
>I realized that there is a number at the beginning of my inpcrd files (something
>like 39150) and that does not exist in a mdcrd file. I suspect that may be a
>Is there an intermediate step before analyzing a trajectory file with imin=5?
>also my sander input file is:
> &cntrl
> imin = 5,
> maxcyc = 1,
> ntb = 1,
> ntr = 0,
> cut = 10
> /
>Thanks in advance...

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Received on Tue Dec 07 2004 - 20:53:01 PST
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