Thanks, Dan. I fixed the problem. There was an extra line at the very
end of *inpcrd*
Best, Vitaly
On Sun, Jun 3, 2012 at 4:04 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I think unless you have an orthorhombic system you actually need 6
> numbers, 3 x Box lengths (x, y, z) and 3 x box angles (alpha, beta,
> gamma). I think this error can also happen if the restart is corrupt
> in some way. If you manually modified the restart file do you maybe
> have an extra newline at the bottom of your restart?
>
> If you would like, send me the topology and restart off-list and I can
> check it for you.
>
> -Dan
>
> On Sun, Jun 3, 2012 at 3:08 PM, Dr. Vitaly V. Chaban <vvchaban.gmail.com> wrote:
>> Dear Amber users -
>>
>> What is the correct format for box dimensions in the inpcrd file?
>>
>> Using the format suggested in http://ambermd.org/formats.html#restart,
>> one can assume that last line of the *inpcrd* should contain three
>> numbers in the same format as coordinates above. However, I am getting
>> the following error -
>>
>> | Run on 06/03/2012 at 15:04:26
>>
>> File Assignments:
>> | MDIN: mdin
>> | MDOUT: mdout
>> |INPCRD: inpcrd
>> | PARM: prmtop
>> |RESTRT: restrt
>> | REFC: refc
>> | MDVEL: mdvel
>> | MDEN: mden
>> | MDCRD: mdcrd
>> |MDINFO: mdinfo
>> | MTMD: mtmd
>> |INPDIP: inpdip
>> |RSTDIP: rstdip
>>
>> |INPTRA: inptraj
>> |
>>
>> Here is the input file:
>>
>> Periodic Dynamics Test Run
>> &cntrl
>> imin = 0,
>> ntb = 2, (periodic system)
>> pres0 = 1, (target pressure in bars)
>> comp = 44.6, (compressibility for NPT)
>> taup = 5.0, (time constant for NPT)
>> ntp=1, (isotropic pressure coupling)
>> igb = 0, ntpr = 100, ntwx = 100,
>> ntt = 3, gamma_ln = 1.0,
>> tempi = 300.0, temp0 = 300.0,
>> nstlim = 100000, dt = 0.001,
>> cut = 16.0
>>
>> /
>>
>>
>> --------------------------------------------------------------------------------
>> 1. RESOURCE USE:
>> --------------------------------------------------------------------------------
>>
>> | Flags: MPI
>> getting new box info from bottom of inpcrd
>> | INFO: Old style inpcrd file read
>>
>> peek_ewald_inpcrd: SHOULD NOT BE HERE
>>
>>
>>
>> So, what can be the reason of failure?
>>
>>
>> Thank you,
>> Vitaly Chaban
>>
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Received on Sun Jun 03 2012 - 14:30:02 PDT
