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 - 13:30:03 PDT
