AMBER Archive (2006)

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

From: Jianhui (tianj_at_rpi.edu)
Date: Wed Aug 30 2006 - 14:48:28 CDT

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?
 
Then what does the EXCLUDED ATOM LIST do?

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
>>
>>
>>-----------------------------------------------------------------------
>>The AMBER Mail Reflector
>>To post, send mail to amber_at_scripps.edu
>>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>
>>
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>

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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu