AMBER Archive (2007)

Subject: Re: AMBER: imin=5 and inptraj

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Sat Aug 11 2007 - 16:37:11 CDT

Is there any chance that your trajectory file is in netcdf or binary format?

These may not be supported by imin=5

Also, in my own input files, I appear to have ntx=5.
> Dear Amber community,
>
> I would like to reanalyze one of my trajectories with the imin=5
> functionality of sander. I read in the archives that amber9 sander does
> not support the -y flag anymore, but that the -x flag should be used
> instead. I cannot get it to work however. Executing the command
>
> sander -i in -o out -p prmtop -c rst -x mdcrd -O
>
> produces no error but finishes instantaneously without doing anything.
> Inspection of the output reveals the following lines:
>
> 4. RESULTS
> --------------------------------------------------------------------------------
>
> POST-PROCESSING OF TRAJECTORY ENERGIES
> Trajectory file ended
>
> Here's the input file:
>
> Energy Calculation
> &cntrl
> imin=5, maxcyc=1,
> dx0=0.00000001, ntpr=1,
> /
>
> What am I doing wrong?
>
> Many thanks in advance,
> Nikola
>
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