[AMBER-Developers] TER card issue with ambpdb

From: Ilyas Yildirim <i-yildirim.northwestern.edu>
Date: Mon, 2 Jul 2012 13:42:53 -0500 (CDT)

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.

   Ilyas Yildirim, Ph.D.
   = Department of Chemistry - 2145 Sheridan Road =
   = Northwestern University - Evanston, IL 60208 =
   = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
   = http://www.pas.rochester.edu/~yildirim/ =

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Received on Mon Jul 02 2012 - 12:00:03 PDT
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