Dear all,
I find that how to use chamber to transfer the psf/crd to top/crd of amber.
Because the format of the three parameters (box%a, box%b and box%c) is
F12.6. Thus you need to use the command like "-box 260.0000000 260.0000000
260.0000000". And this version of chamber still can't be used to transfer
the Croase graind (CG) modes of psf/crd to top/crd of amber.
YT
2014-05-22 17:19 GMT+08:00 Yeng-Tseng Wang <c00jsw00.gmail.com>:
> Dear Ross,
> I have changed the code of psfprm.F90. But the error message still occur.
> I will try to read the code and find how to overcome this problem.
> Thanks your help.
> Yeng-Tseng Wang
>
>
>
> 2014-05-22 11:31 GMT+08:00 Ross Walker <ross.rosswalker.co.uk>:
>
> 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
>> >_______________________________________________
>> >AMBER mailing list
>> >AMBER.ambermd.org
>> >http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
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>
>
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Received on Thu May 22 2014 - 22:00:02 PDT
