Re: [AMBER-Developers] TER card issue with ambpdb

From: David A Case <>
Date: Mon, 2 Jul 2012 15:58:17 -0400

On Mon, Jul 02, 2012, Ilyas Yildirim wrote:

> Assume that you have a protein-DNA system. And assume that you define
> two heavy atom such as AU or AG which are covalently connected to some
> of the residues in protein.
> Assume that one does not include these heavy atoms in a mutated residue
> but explicitly use the 'connect' command in leap to create the covalent
> bonds. If the 'frcmod' includes all the necessary parameters, leap will
> create prmtop and inpcrd files without any issues. Savepdb command will
> also create the rigth sequencing of the system (let's say it is called
> mol.pdb).
> Now, if I use 'ambpdb -p prmtop <inpcrd> inpcrd.pdb', the file created
> is not right (not similar to mol.pdb). This was discussed before (in
> 2005) and the main issue wass because of the way ATOMS_PER_MOLECULE is
> defined in the prmtop file. I can understand that because the AG or AU
> atoms which are connected to proteins explicitly will be included in
> the proteins and they will not be seen

There is an (unstated, I think) restriction on how cross-links can be added
in LEaP: the atoms involved in the resulting molecule(s) must be contiguous
in the Amber atom sequence. Thus, the following should work:


followed by the formation of a bond between chain1 and metal2, and/or between
chain2 and metal2. The the following would not work:


Now, if you make a link between metal1 and chain1, you get a new molecule
(made up of the atoms in chain1 plus metal1) that are not contiguous
in atom sequence. In this case, LEaP doesn't complain, but creates an
incorrect prmtop file (with a bad ATOMS_PER_MOLECULE section.) The
ambpdb program uses this information to create (bad) TER cards; but
the sander/pmemd programs also use this (bad) information in computing
pressures. So, the prmtop file has to be fixed.

Some notes:

1. As Jason points out, the parmed program can diagnose and attempt to fix
this; for the second example above, I'm assuming it would bail out, since
there is no proper fix without completely re-ordering all the molecules.

2. There are other programs that do sanity checks on prmtop files: we need
to assemble these into a single place, ideally something that could be
automatically run when a prmtop file is created in the first place.

3. LEaP should at a minimum refuse to accept an order for which the
ATOMS_PER_MOLECULE section would be wrong. It could also reorder things
to make them correct, although that reordering might not be the one the
user really wants.

4. The analysis above may be wrong or incomplete: there may be times when LEaP
creates bad ATOM_PER_MOLECULE records that cannot be explained by the
reasoning above. If you have such a case, please post an example.


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Received on Mon Jul 02 2012 - 13:00:03 PDT
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