On Mon, Sep 14, 2015, Dr. Robert Molt Jr. wrote:
>
> 1.) The reason the process of covalent unit creation in a helix is
> seemingly different (at least to my naive eye) compared to the tutorial
> on proteins is the linkage. I know how amino acids link internally;
> there is only one way to do it (NHCO formation). I am confused on a
> helix because I am unsure what unit Leap will look for: nucleic acid,
> nucleotide, nucleoside?
Think of LEaP as a bookkeeiping program: it doesn't whether it is dealing with
a protein, a nucleic acid, or anything else. It doesn't know the difference
between a nucleotide, nucleoside, etc.
Here's what it does: it looks at the residue names in your input pdb file, and
tries to match that against the list of units it knows about (which you can
see using the "list" command). When it finds a match, it lines up the atoms
in the pdb with those in the library unit. The *only* time it will try to
"build" the location of atoms is if there are atoms in the library that are
missing in the pdb file. It uses the head and tail atom designations in the
library to decide how (if at all) to covalently bond one residue to the next
one.
`
> but I am unsure what atoms Leap will automatically assume to add
> in to connect.
Hope the above makes this clear: it has nothing to do with chemistry. It will
only "add" atoms if they are in the residue library but are missing in the pdb
file.
>
> 2.) Using just a nucleic acid as the parameterized units...
>
> I understand that most atom types differ only by case (upper/lower)
> between GAFF/Amber style text formatting. However, I am seeing atom
> types in the amber parameterization that I cannot identify. For example:
>
> MASS
> CA 12.010 0.360 same as c2
> C 12.010 0.616 same as c
> HA 1.008 0.135 same as hc
> O 16.000 0.434 same as o
> NA 14.010 0.530 same as na
> H 1.008 0.161 same as hn
> N2 14.010 0.530 same as n3
> NO 0.000 0.000 ATTN, need revision
> DU 0.000 0.000 ATTN, need revision
>
> includes "DU," which I do not know how to identify. This does not seem
> to be a standard Amber designation of an atom, based on what I google
> searched or in the manual? I am guessing I did not ask for Amber
> parameters properly:
DU stands for "dummy": something must have gone rather wrong in running
antechamber. You may need to post the "File.pdb" file you used to get this
example.
....dac
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Received on Mon Sep 14 2015 - 15:30:02 PDT
