AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Aug 21 2006 - 09:19:10 CDT

the NTWR variable controls how often to write the restart file.
what value of ntwr did you use?
also you should use a file editor to check the restart file and see if
it looks normal. The format is described on the amber we page.

priya priya wrote:
> Dear
>
> 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 equil.in -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
> Chandigarh.
>
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