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

From: Ilyas Yildirim <>
Date: Mon, 2 Jul 2012 16:49:08 -0500 (CDT)

> 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.

Dave - When I created the prmtop files for both cases (above), the same
ATOMS_PER_MOLECULE sections were created in both prmtop files. Of course,
atom sequencing are different in both cases, so ambpdb will not create
the same .pdb file.

In sander and pmemd, you wrote that ATOMS_PER_MOLECULE section is used to
compute pressures. If in both prmtop files we have the same
ATOMS_PER_MOLECULE sections, does that mean the pressures calculated will
be the same? Or other sections in prmtop files (combined with the
ATOMS_PER_MOLECULE section) are used in pressure calculation? Thanks.


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Received on Mon Jul 02 2012 - 15:00:02 PDT
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