AMBER Archive (2005)

Subject: Re: AMBER: intramolecular nonbonded interactions in AMBER force field

From: Vineet Pande (pande_vineet_at_hotmail.com)
Date: Thu Apr 21 2005 - 08:26:30 CDT

Dear Prof. Simmerling:
Page 109 and 110 of Amber 8 manual "...Thus the amber mask list is rebuilt
from these 1-1, 1-2, 1-3,
and 1-4 pairs......"
1-3 and 1-4 are understandable...as nonbonded pairs but 1-1 and 1-2 then
correspond to self and bonded interaction?? whats the relevance)
Thanks!
Vineet
>
>I searched the amber 8 manual lfor "1-1" and found nothing.
>What page is this on? I'll look at it and see if I can help explain it.
>Carlos
>
>>>
>>May I comment here and also ask one question related...When we say 1-4
>>nonbonded interactions its clear what it means but when we say 1-1
>>nonbonded interactions (as it is in AMBER manual) what does it mean?
>>Cheerio
>>Vineet.
>>
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