You saved a .crd snapshot from a .crd file (10 numbers per line), and
you're trying to use it as a sander -c file, when a .rst (6
numbers/line, higher precision) is called for.
You could convert the .crd to .rst, or better save it in that format in
the first place.
However, you won't have velocities, so will need to equilibrate from
scratch.
Note to developers: why not just recognize an read a .crd file as if it
were a velocity-free .rst, giving appropriate notice?
Bill
On 11/16/17 6:25 PM, James Kress wrote:
> Is there some part of the Amber documentation that shows how to extract a
> single frame from a trajectory and then use that frame as the -c input for
> another, new MD run?
>
> I've tried
>
> trajout frame1000.crd onlyframes 1000
>
> to extract frame 1000 but the files I get are rejected when I use them in
> the command:
>
> sander -O -I input.in -o output.out -p prmtop.prmtop -c frame1000.crd
>
> ERROR: Problem reading coordinates or velocities from frame1000.crd
>
> I could not understand line 3 :
> 42.500 38.645 31.170 42.986 37.880 30.854 44.290 38.130 31.455
> 44.769
>
> Any assistance would be appreciated.
>
> Jim
>
>
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Received on Thu Nov 16 2017 - 19:00:03 PST
