AMBER Archive (2006)

Subject: Re: AMBER: 1-4 interaction in AMBER8

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Aug 30 2006 - 16:23:26 CDT


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_at_rpi.edu
>>>2006-08-30
>>>
>>>
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>
>= = = = = = = = = = = = = = = = = = = =
>
>Jianhui
>tianj_at_rpi.edu
>2006-08-30
>
>
>
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>

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