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
