Hi Yeng,
It's wrapping on fixed length arrays of 256. (ancient code. :'( ). Try
replacing all occurrences of 256 with 512 in
$AMBERHOME/AmberTools/src/chamber/ recompile and see if that fixes it. I
tried a quick grep and found:
grep 256 *
psfprm.F90: character(len=256), dimension(:), allocatable :: str_files
psfprm.F90: character(len=256) ::
outu_name,psf_filename,prmtop_filename, &
psfprm.F90: character(len=256) :: header
psfprm.F90: character(len=256) :: buf
psfprm.F90: character(len=256) :: buf
But it's late here so there may be more.
Alternatively try a box size of 256x256x256 - that's probably ok accuracy
wise here and may run faster (power of 2 is always good) than 260^3.
All the best
Ross
On 5/21/14, 6:23 PM, "Yeng-Tseng Wang" <c00jsw00.gmail.com> wrote:
>Dear all,
>I used the chamber to transfer the crd/psf to top/crd of amber format.
>And
>My command is " chamber -xpsf step5_assembly.xplor.psf -crd
>step5_assembly.pdb -p amber.top -inpcrd amber.crd -nocmap -str stream
>toppar.str -tip3_flex -box 260 260 260" . But I got the error message,
>this
>message is "FATAL ERROR: Box length must be greater than 4A". I am
>confused
>with this message, because I have set the length of pbc is 260 x 260 x
>260.
>Why the error occur ?
>Thanks for your help
>
>Yeng-Tseng Wang
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>AMBER.ambermd.org
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Received on Wed May 21 2014 - 21:00:02 PDT
