[AMBER] using internal geometry

From: newamber list <newamberlist.gmail.com>
Date: Mon, 2 Mar 2015 18:07:47 +0000

Dear All,

I am sure this is irrelevant question for AMBER but tleap functionality in
AMBERTools does this job. For example if there is any missing atom in the
loaded pdb then tleap can add that missing atom using residue library.

I think this tleap module uses internal geometry (Z matrix) of the residue
and generates a new Cartesian coordinate in space for missing atom. I have
similar problem which I tried to ask in babel community but no reply.

Lets say I have a,b,c,d four atoms (or even more). I can use babel to
generate Z matrix which is internal geometry coordinates. I have many cases
when I need to find Cartesian coordinate of atom 'a' given that I know
Cartesian coordinate for b,c and d (other atoms too).

This is very simple problem but am not able to come up with a solution.
Also a mathematical explanation would help.

kind regards,
AMBER mailing list
Received on Mon Mar 02 2015 - 10:30:03 PST
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