it sounds like you have some general problem in your scripts or input.
I would suggest going step by step in comparing this set of inputs
to ones that you ran successfully before. for example, does the new
prmtop and inpcrd
work with scripts you used before for MD? if you change things one at
a time until you have exactly the same as what worked before then
you will probably find the problem. I can't think of any reason why you would
get no output at all. Are you sure that sander actually starts?
On 7/11/07, Mikyung <seo.ualberta.ca> wrote:
> Hello Carlos,
>
> I ran exact same thing except imin=1 but it didn't work.
> I didn't get any output file and the calculation with newly created
> trajectory seem to be stuck.
> Even though I ran exact same calculation with only one frame, there was
> no output after long time.
> Does new trajectory or new topology have a problem ?
> When I submitted job, there was no error message at all.
>
>
> On 10-Jul-07, at 4:08 PM, Carlos Simmerling wrote:
>
> > 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 Sun Jul 15 2007 - 06:07:03 PDT
