Thank you. A few hours ago I found this document, which goes into a lot more detail about the format (
http://ambermd.org/prmtop.pdf).
I’ll merge and cross-check responses against it. Once I get something running I’ll do validation.
Best,
.Chris.
> On Sep 21, 2016, at 4:09 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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 - 13:30:05 PDT
