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

From: priya priya <>
Date: Mon, 21 Aug 2006 08:46:29 +0100 (BST)

  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 /usr/local/amber8/exe/equil1.rst

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 - 06:07:07 PDT
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