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

From: Dhruva Chakravorty <>
Date: Mon, 2 Jul 2012 16:23:33 -0400


Just so we are all clear on this, what is the correct sequence when both metals bind o both chains, i.e. metal1 and metal2 bind to both chains 1 and 2 as well ?

With regards


On Jul 2, 2012, at 3:58 PM, David A Case wrote:

> 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:
> chain1
> metal1
> chain2
> metal1
> followed by the formation of a bond between chain1 and metal2, and/or between
> chain2 and metal2. The the following would not work:
> chain1
> chain2
> metal1
> metal2
> 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.
> ...dac
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Received on Mon Jul 02 2012 - 13:30:03 PDT
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