Hi Wang,
Do you mean you want to have some kind of infinite polymer? I.e. like a
covalent surface that is then solvated in water? If so then unfortunately
AMBER can't do this at present and you would have to modify the code
yourself to do it. I believe that CHARMM can probably do it but I have never
tried it.
Good luck,
Ross
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of WANG,YING
> Sent: Friday, May 23, 2008 6:17 PM
> To: amber.scripps.edu
> Subject: AMBER: periodic bondary condition
>
> Hi, Dear Ambers,
>
> I solvate my specimen in explicit water, like TIP3P box. I let the
> buffer to be 8 angstrom. If I want to let some of the covalent
> bond across the periodic boundary condition, could anybody tell me
> how to acchieve it? Thanks very much in advance!!
>
>
>
> Best,
>
>
> Ying
>
>
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Received on Sun May 25 2008 - 06:08:03 PDT
