it looks like it might be that the coordinates are too large to fit the
restart format. you can confirm by visually inspecting the restart file and
looking for * characters.
it usally happens in a long run because the water diffuses so far from the
origin. this can be avoided in long runs by turning on wrapping (iwrap=1)
2009/7/1 Jeffrey <jeffry20072008.yahoo.cn>
> Dear AMBER users,
>
> I performed a long md simulation by repeating restarts. But at the 28th
> segment, the simulation can't be continued because the pmemd can't open the
> restart file (npt28.rst). Here are some error message:
> in .out file:
> ---
> ....
> &cntrl
> imin=0,
> ntx=5, irest=1,
> ntpr=100, ntwx=1000,ntwr=5000,
> dt=0.002,nstlim=1000000, nscm=1000,
> cut=9.,dielc=1.0,
> ntc=2, ntf=2,
> ntb=2,
> ntp=1,pres0=1.0,taup=3.0,
> ntt=1, tautp=3.0,temp0=300.0,
> ioutfm=1
> /
> | ERROR: Could not read coords from npt28.rst
> ---------------
>
> When using ambpdb to convert from npt28.rst to npt28.pdb using the command:
> ambpdb -p mono10.prmtop < npt28.rst > npt28.pdb
>
> errors are:
> ------------
> | New format PARM file being parsed.
> | Version = 1.000 Date = 05/19/09 Time = 22:55:51
> forrtl: severe (64): input conversion error, unit 5, file stdin
> Image PC Routine Line Source
> ambpdb 00000000004A593E Unknown Unknown Unknown
> ambpdb 00000000004A4B3E Unknown Unknown Unknown
> ambpdb 000000000045498A Unknown Unknown Unknown
> ambpdb 000000000041E172 Unknown Unknown Unknown
> ambpdb 000000000041D9A1 Unknown Unknown Unknown
> ambpdb 0000000000439716 Unknown Unknown Unknown
> ambpdb 000000000040D194 Unknown Unknown Unknown
> ambpdb 00000000004058FD Unknown Unknown Unknown
> ambpdb 00000000004034CC Unknown Unknown Unknown
> libc.so.6 0000003083C1D8A4 Unknown Unknown Unknown
> ambpdb 00000000004033D9 Unknown Unknown Unknown
> -----------
>
>
> Does anyone encounter the similar problems?
> Any suggestion is greatly appreciated.
>
> Thanks.
>
>
> Jeffry
>
>
> -----------
> Dalian Institute of Chemical Physics,
> Chinese Academy of Sciences
> Dalian, China
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>
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Received on Mon Jul 06 2009 - 12:27:20 PDT
