Hi Rashid,
Thank you for the input. It worked fine with scnb and scee flags removed and submission with -y instead of -x.
Regards
Sowmya
________________________________
From: Abdul-Rashid III Sampaco <absampaco.up.edu.ph>
Sent: Wednesday, November 29, 2017 2:22:37 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Post processing of trajectory
>From what I understand from the tutorial, they want to calculate energies
of the structures in the file "*alav-sm.crd*".
I recommend using this command instead.
$AMBERHOME/exe/sander -O -i min.in -o min.out -p ../metp8.top -y
../prep/alav-sm.crd -c ../min.rst
The -y flag is used for input of the structures you want to analyze.
In this case, the -x flag is not needed since you are performing energy
minimization on the structures, hence you don't need to write out a new
trajectory file.
Rashid
On Wed, Nov 29, 2017 at 9:04 PM, Sowmya Indrakumar <soemya.kemi.dtu.dk>
wrote:
> Dear Amber users,
>
> I'm following this tutorial : http://spider.irb.hr/
> tutorial2/Tutorial2.htm#_C)_Extracting_the_Total_Energies
>
>
> Under *Evaluating the energies using an implicit scoring function*, they
> calculate the energy of every frame using the following as input parameters:
>
>
> imin=5 post processing of trajectory
> &cntrl
> imin=5,
> ntx=1,
> maxcyc=1,
> ntb=0,
> ntc=1,
> ntf=1,
> ntwx=1,
> ntwe=0,
> ntwr=1,
> ntpr=1,
> ntt=1,
> cut=999,
> scnb=2.0,
> scee=1.2,
> igb=2,
> intdiel=1.0,
> extdiel=78.5,
> gbsa=1,
> &end
>
>
> and submit the job using the following the command:
>
> $AMBERHOME/exe/sander -O -i min.in -o min.out -p ../metp8.top -x
> ../prep/alav-sm.crd -c ../min.rst
>
>
> When I run this, I get this messsage in the output file (-o): error in
> reading namelist cntrl
>
>
> When I try the same input file with imin=1, it calculates the energy for
> one structure.
>
> Also, when the scnb and scee flags are removed with imin=5, I get the
> following message: Error opening unit 24: File "inptraj" is missing or
> unreadable
>
> Is there any problem with the input file?
>
> Any help is appreciated.
>
> Thanks.
>
> Regards
>
> Sowmya
>
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Received on Wed Nov 29 2017 - 06:00:03 PST
