On Wed, Aug 21, 2013 at 11:03 AM, Jose Borreguero <borreguero.gmail.com>wrote:
>
> %FLAG
> BOND_FORCE_CONSTANT
> %FORMAT(5E16.8)
>
> 3.40000000E+02 1.89650000E+02 3.50120000E+02
>
> W
> hile the second once contains:
> %FLAG
> BOND_FORCE_CONSTANT
> %FORMAT(5E16.8)
>
> 3.50120000E+02 3.40000000E+02 1.89650000E+02
>
> Looks like the values are shuffled, but that would imply that the ordering
> of the atoms has changed. However, the two prmtop files are indentical when
> looking at the %FLAG ATOM_NAME section.
>
The shuffling does not imply that the atom ordering has changed, although
it is admittedly misleading. Determining the equivalence of two topology
files is actually pretty difficult. All this shuffling means is that the
the bond force constant are shuffled (not much information there ;)).
These values are addressed via pointers in BONDS_WITHOUT_HYDROGEN and
BONDS_INC_HYDROGEN (see
http://ambermd.org/formats.html for more
information). The BONDS_WITHOUT_HYDROGEN and BONDS_INC_HYDROGEN assign an
index into the BOND_FORCE_CONSTANT and BOND_EQUIL_VALUE arrays for each
bond (that is defined by 2 atom indexes). Therefore, if you shuffle the
BOND_FORCE_CONSTANT section, all you have to do is adjust the assigned
indices in BONDS_WITHOUT_HYDROGEN and BONDS_INC_HYDROGEN.
You can use the "print*" commands in ParmEd (printBonds, printAngles,
printDihedrals, printDetails) to verify this (or even more definitively,
use sander to compute the energy using both topology files and see that
they are identical).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 21 2013 - 09:00:02 PDT
