AMBER Archive (2005)

Subject: AMBER: Lennard-Jones coeff...

From: Pavan G (pavanamber_at_gmail.com)
Date: Tue Aug 30 2005 - 15:26:49 CDT

Hi all,

I've built a system consisting of Glycerol, Lysozyme and water which
gives me a total of 17 distinct types of atoms (NTYPES) and 153
different Lennard-Jones A coefficents which is = (17*(17+1))/2.
So I understand that if I name my 17 atoms as 1 through 17,
the first entry in the Lennard Jones A coeff FLAG in a prmtop file
corresponds to
1-1 interaction ---> first entry
1-2 interaction----> second entry
17-16 interaction ----> 152nd entry
17-17 interaction -----> 153rd entry

Now, here is my question.
In what order are the 17 distinct atom types arranged.
i.e what is the atom_type[1] == ?
what is the atom_type[17] == ?

and what are the 17 distinct types. I understand that we get 2 types
(H-O-H and O-H) from water, and 5 types (C-O-H, O-H, C-H, H-C-H,
C-C-C) from Glycerol. So, that leaves 10 distinct types in
Lysozyme[O-H in glycerol and water are not similar]. Well, Lysozyme
could have more than 10 considering the fact that some of its atoms
are the same as those already represented by water and glycerol.
The pdb file does give the complete set of atom types, but are not
distinct. How can I find the set of distinct atom types in Lysozyme?

Thanks for your time.
Pavan
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