AMBER Archive (2004)

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

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Thu Apr 22 2004 - 07:02:30 CDT

>===== Original Message From Ilyas Yildirim <yildirim_at_pas.rochester.edu> =====
>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?

Yes - antechamber will calculate connectivity from internal tables of
single/double/triple bond lengths. Look for atomvalnum and comments
like "triple bond" in bcctype.c

> Or do we have to specify the connections, too?

These are calculated in the same manner - by distances.

So, it is importantant that your starting .pdb have reasonably correct
bond distances. If you create your molecule in an interactive graphics
package, be sure to minimize the structure in the package's force field - even
though it will be crude relative to AMBER.

>(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)

Basically - yes.

>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.

I think you are on the right track - just keep in mind that the format was
designed in the days of the fixed width punched card - so column positions
are very important.

Look at lots of crystal structures. If you "get" ATOM, HETATM, and TER, you
are well on your way to getting a molecule into antechamber.

Chris

Chris Moth
chris.moth_at_vanderbilt.edu

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