AMBER Archive (2009)

Subject: Re: [AMBER] Specifying improper dihedrals

From: Mark Williamson (mjw_at_sdsc.edu)
Date: Wed Jun 17 2009 - 12:12:08 CDT

Ben Roberts wrote:

> becomes
>
> <snip>
> 34623 34647 -34620 -34611 43 20088 20094 20091
> -0 44
> 21228 21237 21234 -0 44 15294 15303 15300
> -3 44
> 15402 15411 15408 -3 44
> %FLAG EXCLUDED_ATOMS_LIST
> <snip>
>
> Which is all well and good, but when I ran "rdparm dihedrals" on this
> file, it marked the new dihedrals - which is fine - but only the second
> two showed up as impropers (i.e., with an I before them).
>
> Output from rdparm:
>
> <snip>
> 45137: 1.000 3.14 2.0 :448_at_CG :448_at_CE1 :448_at_ND1 :1_at_NI
> (6697,6699,6698,1)
> 45138: 1.000 3.14 2.0 :474_at_CE1 :474_at_CD2 :474_at_NE2 :1_at_NI
> (7077,7080,7079,1)
> I 45139: 1.000 3.14 2.0 :336_at_CE1 :336_at_CD2 :336_at_NE2 :2_at_NI
> (5099,5102,5101,2)
> I 45140: 1.000 3.14 2.0 :338_at_CE1 :338_at_CD2 :338_at_NE2 :2_at_NI
> (5135,5138,5137,2)
> <snip>
>
> Now I know that to specify an improper, one makes the fourth number
> negative - as you can see I've done. But it looks to me as though,
> because that fourth number is zero in this case, it's interpreted it as
> a non-negative number!
>
>
> Is there any way around this?
>
> Cheers,
> Ben
>

Hi Ben,

I recently hit a similar issue when coding the the CHAMBER CHARMM to
AMBER converter. In short, my solution was to reverse the atom index
order in the dihedral:

20088 20094 20091 -0 44

would become

-0 20091 20094 20088 44

I think this same approach may work for you; test it and see if it works
as expected.

Here's the cvs log for my CHAMBER check-in; it should give some background:

revision 10.49
date: 2009/05/26 20:18:02; author: mjw; state: Exp; lines: +31 -6
MJW:

Fix a situation when the k value of a prmtop is zero and negative
==================================================================

Within the sections:

         DIHEDRALS_INC_HYDROGEN
         DIHEDRALS_WITHOUT_HYDROGEN

in a prmtop file, dihedrals are listed for a system being described.
Each dihedral is described using five numbers, the first four relate to
the indexes of the atoms in the dihedral and the fifth is a "pointer"
into the DIHEDRAL_FORCE_CONSTANT, DIHEDRAL_PERIODICITY and
DIHEDRAL_PHASE lists giving the associated parameters for that specific
dihedral.

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.

For example, the dihedral listed in a prmtop as follows:

%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10i8)
        0 12 18 24 2

would correspond to torsion 1-5-7-9 and point to number two in the
associated DIHEDRAL_* parameter lists.

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.

A problem arises when k is atom one (1) 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

IEEE 754 does not yield a solution here since there is debate about
the formatted printing of negative zeros.

Hence the solution is to *reverse* the dihedral, hence in this example,
the dihedral written to the prmtop will be:

18 0 -6 9

Thanks to Dave Case, Gustavo, Wei and Ross for discussions on this.
----------------------------

I hope this helps,

Mark

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