AMBER Archive (2004)

Subject: AMBER: What kind of informations are needed in a .pdb file in order to start using antechamber?

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Apr 21 2004 - 23:51:40 CDT

Dear AMBER Members,

I had a technical question about .pdb files. Is it enough to specify just
the atom names and the coordinates of each atom in a molecule in order to
start using antechamber? Or do we have to specify the connections, too?
(Or some other things that antechamber or leap needs) The way I am
thinking is as following: If you specify the types of the atoms, and the
coordinates of each atom, respectively, you have a 3D picture of the
molecule in the space, without having the connections. If there are some
special situations like some particular charge combinations in the
molecule, they can be specified too. So, it seems to me that, assuming
there are not any special cases present in the molecule, specifying the
atom names and each coordinates are enough to start using antechamber. (At
the end, depending on the model we want to use, we can find the charges,
as it is the case when RESP is used)

Best,

PS: Are there any good references on understanding the .pdb files? I have
checked out www.pdb.org and they have information about reading/writing a
.pdb file, but it seems a little bit confusing. Any suggestion is
appreciated. 

-- 
  Ilyas Yildirim
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