Hi,
I'll do my best to answer these questions - corrections from others are welcome.
On Wed, Sep 21, 2016 at 1:10 PM, Christian Schafmeister
<drschafmeister.gmail.com> wrote:
>
> QUESTION #1: The excluded atom lists are indices into the atom tables in increasing numerical order?
I think so, yes (related to #2).
> QUESTION #2: The excluded atom list only includes indices (j) where j>i for atom_i?
Yes.
>
> QUESTION #3: Excluded atoms are 1-2 (stretch) and 1-3 (angle) interactions What about 1-4 (dihedral) interactions, are they in the EXCLUDED_ATOMS_LIST or not?
Yes 1-4 interactions are excluded.
>
> QUESTION #4: Is there anything important I’m missing about non-bonded interactions? Magical negative indices or values or something that have special meaning?
A negative index in NONBONDED_PARM_INDEX means HB term, otherwise it's
a LJ term (mentioned in the docs).
-Dan
>
> Please correct anything that I’m saying wrong above.
>
> Christian Schafmeister
> Professor, Chemistry Department
> Temple University
> meister.temple.edu <mailto:meister.temple.edu>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Sep 21 2016 - 13:30:04 PDT
