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

From: Jason Swails <>
Date: Mon, 2 Jul 2012 15:16:10 -0400

On Mon, Jul 2, 2012 at 2:42 PM, Ilyas Yildirim

> I think this issue was discussed before in amber mailing list but I want to
> double check on one thing:
> 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. There is a tutorial in the amber website (created by Ross) that is
> almost similar to this system except that the heavy atoms are included in a
> mutated residue, which is created by the user.
> 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
> as single ions by ambpdb (like the Na+ or Cl- ions). As a result, TER cards
> will be put to the wrong places by ambpdb.
> The question I have is the following: Will this effect the computations or
> the
> only effect of this way of creating the prmtop/inpcrd files is on ambpdb
> putting the TER cards to the wrong places? I will expect that there should
> not
> be any issue with the computations but the TER cards placed by ambpdb while
> creating the .pdb files. Am I correct? Thanks.

I'm not sure exactly what's going wrong here. Is ATOMS_PER_MOLECULE not
being defined correctly? I know this can happen in tleap sometimes when
two independent 'molecules' are connected via the 'bond' command, and to
date I don't think the source of this error has been determined or fixed
(given there are acceptable workarounds).

If the ATOMS_PER_MOLECULE section is *wrong*, then things can go very wrong
in both pmemd and sander. A check was introduced in Amber 12 to guard
against one manifestation of this bug (namely, adding up all numbers in the
ATOMS_PER_MOLECULE section must sum to NATOM). If this section is
*seriously* wrong, then pressure scaling may be thrown out of whack (to
what degree, I'm not sure). pmemd also uses this section to designate PRFs
(pseudo-residue fragments -- part of the parallel load balancing it does)... both have a function (setMolecules) that will fix the
ATOMS_PER_MOLECULE section (or bail out of the prmtop is set up in such a
way that the ATOMS_PER_MOLECULE section cannot be made correctly). After
doing this, the TER cards should be put in the correct place.

If the problem lies in ambpdb, on the other hand, then the only issues you
may see is when you load the PDB back into tleap. Without TER cards
between molecules, it will recognize polymer units (i.e. nucleic acid
residues and amino acid residues) as in-chain, and will not appropriately
pick up the terminal residue (e.g., C- or N-terminus for amino acids).


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Mon Jul 02 2012 - 12:30:02 PDT
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