CPPTRAJ: Trajectory Analysis. V17.00
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| Date/time: 11/13/17 17:30:53
| Available memory: 3.696 GB
Loading previous history from log 'cpptraj.log'
> parm bay.prmtop
Reading 'bay.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
> list parm
PARAMETER FILES (1 total):
0: bay.prmtop, 30230 atoms, 9254 res, box: Orthogonal, 9069 mol, 9053
solvent
> trajin md1.mdcrd.gz
Reading 'md1.mdcrd.gz' as Amber Trajectory
Warning: md1.mdcrd.gz: Number of frames in compressed traj could not be
determined.
Warning: Frames will be read until EOF.
> list trajin
INPUT TRAJECTORIES (1 total):
0: 'md1.mdcrd.gz' is an AMBER trajectory, Parm bay.prmtop (Orthogonal
box), unknown #frames, start=0 offset=1
Total number of frames is unknown.
On Mon, Nov 13, 2017 at 5:30 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> No it gives error immediately. It did not run for any length.
>
> On Mon, Nov 13, 2017 at 5:24 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> Did it run for any length of time? Was the cpu busy? Was there any other
>> output?
>>
>>
>> On 11/13/17 4:22 AM, Rana Rehan Khalid wrote:
>> > yes sir program is stop.
>> >
>> > On Mon, Nov 13, 2017 at 4:33 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>> >
>> >> Do you see the cpu in use from the program?
>> >>
>> >> $ top
>> >>
>> >> Bill
>> >>
>> >>
>> >> On 11/13/17 3:32 AM, Rana Rehan Khalid wrote:
>> >>> No its not stop . One maybe issue i am not sure that I ran the
>> simulation
>> >>> on amber 14 which is install on our cluster while in my laptop it is
>> >> amber
>> >>> 17 and I start analysis on my laptop. Thanks
>> >>>
>> >>> On Mon, Nov 13, 2017 at 4:26 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>> >>>
>> >>>> Did the program stop? Was there any other output?
>> >>>>
>> >>>> Bill
>> >>>>
>> >>>>
>> >>>> On 11/13/17 3:24 AM, Rana Rehan Khalid wrote:
>> >>>>> Dear Amber users
>> >>>>>
>> >>>>> I am facing this error. I have just started the analysis on my mdcrd
>> >>>> files
>> >>>>> and face this issue kindly guide how can i resolve it. I already run
>> >> the
>> >>>> 20
>> >>>>> ns simulation and now start its analysis when i open the first file
>> >> these
>> >>>>> warning messages show.
>> >>>>>
>> >>>>> parm bay.prmtop
>> >>>>> Reading 'bay.prmtop' as Amber Topology
>> >>>>> Radius Set: modified Bondi radii (mbondi)
>> >>>>>> trajin md1.mdcrd.gz
>> >>>>> Reading 'md1.mdcrd.gz' as Amber Trajectory
>> >>>>> Warning: md1.mdcrd.gz: Number of frames in compressed traj could
>> not be
>> >>>>> determined.
>> >>>>> Warning: Frames will be read until EOF.
>> >>>>>> list
>> >>>>> trajin
>> >>>>>
>> >>>>>
>> >>>>> INPUT TRAJECTORIES (1 total):
>> >>>>> 0: 'md1.mdcrd.gz' is an AMBER trajectory, Parm bay.prmtop
>> >> (Orthogonal
>> >>>>> box), unknown #frames, start=0 offset=1
>> >>>>> Total number of frames is unknown.
>> >>>>>
>> >>>>> Regards
>> >>>>> _______________________________________________
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Received on Mon Nov 13 2017 - 05:00:03 PST
