Jianhui wrote:
>Hello Carlos,
>
>Thank you for your quick answer. That means:
> dihedral 1-4 pairs
>1-2-3-4 1-4
>2-3-35-36 2-36
>1-4 pairs are just converted from the dihedral lists.
>Right?
>
>
>
right, except that there is some duplication in the dihedral list
(multiple dihedral
terms for each set of 4 atoms, as well as duplicates in rings) so not
all dihedrals
have 1-4 energies calculated
>Then what does the EXCLUDED ATOM LIST do?
>
>
>
this specifies which atoms should NOT interact (usually because they have
bonds or angles that account for their interaction).
>Best regards,
>
>======= At 2006-08-30, 15:22:13 you wrote: =======
>
>
>
>>they are calculated using the list of atoms that define the dihedral angles.
>>the same atoms are used for vdw and ele.
>>
>>
>>
>>Jianhui wrote:
>>
>>
>>
>>>Hi AMBER users,
>>>
>>>I looked up in the AMBER8 manual but didn't find the description about how the 1-4 interaction are calculated. For the 1-4 interaction calculation, how does AMBER8 know which are the 1-4 pairs? Does the 1-4 pairs for 1-4 Lennard-Jones and 1-4 Coulomb interaction the same? Thanks a lot.
>>>
>>>Best regards,
>>>
>>>Jianhui
>>>tianj.rpi.edu
>>>2006-08-30
>>>
>>>
>>>-----------------------------------------------------------------------
>>>The AMBER Mail Reflector
>>>To post, send mail to amber.scripps.edu
>>>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>>
>>>
>>>
>>>
>>-----------------------------------------------------------------------
>>The AMBER Mail Reflector
>>To post, send mail to amber.scripps.edu
>>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>
>>
>>
>>
>
>= = = = = = = = = = = = = = = = = = = =
>
>Jianhui
>tianj.rpi.edu
>2006-08-30
>
>
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Sep 03 2006 - 06:07:07 PDT
