RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8

From: Ross Walker <>
Date: Mon, 21 Aug 2006 08:48:00 -0700

Dear Priya,
Have you looked at the restart file to see if you can see what is wrong with
it. Are there any *'s in the output file suggesting that your system drifted
away from the original origin by too far? Have you visualized the
trajectory? Does anything look wrong? Did your system blow up or did it
remain stable?
Check if you set nscm to a reasonable value. If you are running this system
in implicit solvent you probably need to set nscm=1000 or so to remove
center of mass motion. Without doing this your system can drift a long way
from the origin such that the coordinate values exceed the available space
in the output and restart files.
Alternatively your restart file may have simply got corrupted due to
hardware issues with your computer system. Without more details about the
specific problem we can't help much more I am afraid.
All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
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From: [] On Behalf Of
priya priya
Sent: Monday, August 21, 2006 00:46
Subject: AMBER: problem relating all atom structure prediction and folding
simulations on AMBER8

I am doing the first stage of the simulation on 42 residue peptide at 325 K.
Running 50 ns of simulation at 325 K in 10 stages of 5 ns each.
Input file reads as follows:
Stage 2 equilibration 1 0-5ns &cntrl imin=0, irest=1, ntx=5,
nstlim=2500000, dt=0.002, ntc=2, ntf=2, ntt=1, tautp=0.5,
tempi=325.0, temp0=325.0, ntpr=500, ntwx=500, ntb=0, igb=1,
cut=999.,rgbmax=999. /
The commannd used for running simulation is
$AMBERHOME/exe/sander -O -i -p TC5b.prmtop -c heat7.rst -r
equil1.rst -o equil1.out -x equil1.mdcrd
first step run well for 5 days but the rst file is not complete. when i run
the next step of 5ns it gives an error as
forrtl: severe (64): input conversion error, unit 9, file
so now i am

 unable to proceed further will be somebody guide me.
With Regards
Priya Anand
Department of Biophysics
Panjab University


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Received on Wed Aug 23 2006 - 06:07:10 PDT
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