> I restarted my simulation again this time in explicit solvent but after
> running 210 ns it again shows the same problem that it could not read the
> coordinates. I tried with so many different ways is there any way to
> restart my job. I have attached the topology and restart file which has
> problem and the input file as well.
> Kindly have a look.
>
> Thanks
>
>
>
> On 21 June 2012 17:09, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> This is happening because the coordinates are overflowing, either
>> because the system is massive or part of it has moved far away from
>> the coordinate origin. Not knowing the specifics of your system I
>> can't be sure, but it appears that this problem is with the last atom
>> in your system, which appears to be very far away from everything else
>> for some reason. If you are using Amber12 you can use the new netcdf
>> restart file format (ntxo = 2, see http://ambermd.org/doc12/ for a
>> little more info) which can hold larger numbers than the ASCII restart
>> format. Note that netcdf restarts are currently only supported by
>> Amber12 sander, pmemd, cpptraj, and NAB.
>>
>> -Dan
>>
>> On Wed, Jun 20, 2012 at 3:34 PM, Ashutosh Shandilya
>> <izerokelvin.gmail.com> wrote:
>> > Dear Amber users
>> >
>> > The coordinate file after simulation (implicit) is showing star mark
>> > highlighted in the first column. I reran the simulation but again it
>> shows
>> > the same error and one more observation was that the (x,y,z) coordinate
>> > values are quite high from the original one. To generate a pdb file if I
>> > manually give some arbitrary similar value instead of stars and again
>> > restart the simulation its giving nan values.
>> >
>> > 1184.6077849 87.8888422 467.84796201185.3934567 87.3155358 466.8924446
>> > 1185.2680706 88.7090605 464.54429731186.4476164 89.0831923 464.6623140
>> > 1184.8475718 87.6484031 463.75189751183.8646739 87.4420910 463.7650775
>> > 1185.7071448 86.8318350 462.86466941185.0671587 86.3891983 462.1111381
>> > 1186.3153669 87.5821378 462.35431881186.6158655 85.8276403 463.4688349
>> > 1187.5664425 85.4647477 462.72178371186.3922755 85.4288019 464.6323917
>> > ************* *-48.0818384-390.5949655
>> > 0.0068848 0.0591804 -0.1366963 1.8340742 -0.6580615 -0.6321001
>> > -0.6970049 0.0615980 -0.9000795 1.2015969 0.2187631 -0.5411940
>> > 0.1566680 0.3761406 -0.5256694 -0.7715472 -1.1329467 -0.3315136
>> > 0.8764598 0.0811084 1.0273480 0.2398398 -0.1928732 -0.0443124
>> > -0.0285152 0.3707692 -0.1225974 -0.0579449 -0.2956305 -0.2325728
>> > 0.4026198 0.3070977 0.2775148 -0.3166358 -0.2877791 0.1805477
>> >
>> > If some one came across this problem and have any clue that would help.
>> > Thanks
>> > Ashutosh
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Lab Specialist
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-9119 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Thu Jul 12 2012 - 11:30:02 PDT
