Re: [AMBER-Developers] 1-4 Duplicate NB flagging when k atom index is one

From: Gustavo Seabra <>
Date: Fri, 22 May 2009 01:34:05 +0100

On Thu, May 21, 2009 at 4:33 PM, Mark Williamson <> wrote:
> The first four numbers are not (as one would expect) the atom index (given
> by the order in ATOM_NAME) of each atom in the dihedral, but instead the
> atom index number minus one, multiplied by three.

:-) Any idea as to why that is?

> AMBER denotes an IMPROPER torsion in its dihedral indexes by prefixing the
> 4th atom (l) with a negative sign. It does the same with the 3rd atom (k)
> to indicate that the end group interactions (i.e. any 1-4 interactions) of
> this torsion should be ignored.
> My question is, what happens when k is atom one in the system and it needs
> to be flagged to ignore its 1-4 contribution, e.g. :
> Given a dihedral of atom index: 4-3-1-7
> it becomes the prmtop'ed form of:  9           6           0          18
> Here in lies the problem, you cannot put a sign on a zero:
> 9           6          -0          18

1. Is it possible to redefine that dihedral so that atom one does not
fall in the third or fourth position?

2. If this is a problem only when reading the prmtop (if you flag that
atom yourself), maybe changing the code to first read it as string,
check for the "-" sign, then converting the number to int?

3. If this problem also shows up when writing the prmtop, maybe a
similar thing to (2) could also be done by modifying the code (LEaP?)
to build a string before printing to the prmtop file?


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Received on Fri May 22 2009 - 01:10:52 PDT
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