did you get my suggestion from earlier today?
does everything work with the exact same setup and imin=1?
On 7/10/07, Mikyung <seo.ualberta.ca> wrote:
> Hello amber users,
>
> I tried to extract energy of protein from protein-sugar interaction MD
> trajectory using imin=5.
> As Carlos said, I used "-x" option to read the previous trajectory and
> calculate energy for protein only.
>
> What I did are:
>
> 1. MD simulation of protein-sugar in the gas phase
> 2. strip sugar from trajectory and save to new trajectory
> (MDtraj_protein.x) using ptraj
> 3. create topology (protein.top) and coordinates (protein.crd) files
> for protein only in xleap
> 4. load new trajectory using imin=5 and calculate energy
>
> Here are input and command to run calculation:
>
> &cntrl
> imin = 5, ntx = 1, maxcyc=1,
> scnb = 2.0, scee = 1.2,
> cut = 9999.0
> /
>
> sander -O -i proteinE.in -o proteinE.out -p protein.top -c protein.crd
> -x MDtraj_protein.x
>
> However, I don't get any output file.
> There is nothing in proteinE.out file.
> What is wrong with my input or command?
>
> Is there anyone to have same problem and can you help me?
>
> Thanks
>
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Received on Wed Jul 11 2007 - 06:07:53 PDT
