AMBER Archive (2009)

Subject: RE: [AMBER] Help with torsions in parm99.dat file

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Mar 06 2009 - 18:52:05 CST

Hi Brent,

This was apparently added by me to the AMBER 9 CVS tree on July 27th 2005
and was thus released as part of AMBER 9 and subsequently ambertools. Here
is the log message from the tree:

revision 8.2
date: 2005/07/27 19:25:40; author: rcw; state: Exp; lines: +1 -0
RCW: Explicitly added HC-CT-C-O 0.0 0.0 2.0 term which explicitly defines
one of the options of the X-C-CT-X term. Xleap misbehaves here for NMA and
only gets two of the three HC's. So you get a total of 24 dihedrals for NMA
when there should be 25. This fixes that but means that there is still an
underlying problem with xleap and wildcards even for proteins. While this
fix doesn't affect the energies as is if the barrier height was changed to
something other than 0.0 (e.g. by fitting) then we would have a big problem
without this term being explicitly defined.

I came across this while writing code that would adjust the barrier heights
while trying to automatically fit the force field to underlying quantum
data. The issue, I believe was that Xleap wasn't handling the wildcard terms
correctly. This was to force leap to ignore the wildcard term here.

I agree that it probably should have -2.0 specified in that it should run,
for pn -1.0, -2.0, 3.0, however the specification of the minus sign in the
parm99.dat file is a left over from the days of prep, link, edit and parm.
Leap does not, as far as I can tell, interpret the minus sign in the parm
file and instead deals with duplicate dihedrals internally by running over
the bond list. I should probably update the parm99.dat file for the next
release of ambertools to just be consistent though.

I checked the following options with the current development version of
xleap (which should be similar to the AmberTools 1.2 version):

1) parm99.dat file as released in AMBER 10

source leaprc.ff99SB
mol = sequence { ACE NME }
saveamberparm mol prmtop inpcrd

rdparm prmtop
printdihedrals

This gives:

...
       6: 0.800 0.00 1.0 :1_at_HH33 :1_at_CH3 :1_at_C :1_at_O (4,2,5,6)
E 7: 0.000 0.00 2.0 :1_at_HH33 :1_at_CH3 :1_at_C :1_at_O (4,2,5,6)
E 8: 0.080 3.14 3.0 :1_at_HH33 :1_at_CH3 :1_at_C :1_at_O (4,2,5,6)
...
      10: 0.800 0.00 1.0 :1_at_HH32 :1_at_CH3 :1_at_C :1_at_O (3,2,5,6)
E 11: 0.000 0.00 2.0 :1_at_HH32 :1_at_CH3 :1_at_C :1_at_O (3,2,5,6)
E 12: 0.080 3.14 3.0 :1_at_HH32 :1_at_CH3 :1_at_C :1_at_O (3,2,5,6)
...
      15: 0.800 0.00 1.0 :1_at_HH31 :1_at_CH3 :1_at_C :1_at_O (1,2,5,6)
E 16: 0.000 0.00 2.0 :1_at_HH31 :1_at_CH3 :1_at_C :1_at_O (1,2,5,6)
E 17: 0.080 3.14 3.0 :1_at_HH31 :1_at_CH3 :1_at_C :1_at_O (1,2,5,6)
...
Total = 25 torsions

Replacing the 3 lines in the parm file with:

HC-CT-C -O 1 0.80 0.0 -1. Junmei et al,
1999
HC-CT-C -O 1 0.00 0.0 -2. Explicit of wild
card X-C-CT-X
HC-CT-C -O 1 0.08 180.0 3. Junmei et al,
1999

And repeating the above gives:

...
       6: 0.800 0.00 1.0 :1_at_HH33 :1_at_CH3 :1_at_C :1_at_O (4,2,5,6)
E 7: 0.000 0.00 2.0 :1_at_HH33 :1_at_CH3 :1_at_C :1_at_O (4,2,5,6)
E 8: 0.080 3.14 3.0 :1_at_HH33 :1_at_CH3 :1_at_C :1_at_O (4,2,5,6)
...
      10: 0.800 0.00 1.0 :1_at_HH32 :1_at_CH3 :1_at_C :1_at_O (3,2,5,6)
E 11: 0.000 0.00 2.0 :1_at_HH32 :1_at_CH3 :1_at_C :1_at_O (3,2,5,6)
E 12: 0.080 3.14 3.0 :1_at_HH32 :1_at_CH3 :1_at_C :1_at_O (3,2,5,6)
...
      15: 0.800 0.00 1.0 :1_at_HH31 :1_at_CH3 :1_at_C :1_at_O (1,2,5,6)
E 16: 0.000 0.00 2.0 :1_at_HH31 :1_at_CH3 :1_at_C :1_at_O (1,2,5,6)
E 17: 0.080 3.14 3.0 :1_at_HH31 :1_at_CH3 :1_at_C :1_at_O (1,2,5,6)
...
Total = 25 torsions

Which is the same thing implying that leap doesn't care about the minus
signs on the periodicity.

Repeating this again but with the following:

HC-CT-C -O 1 0.80 0.0 -1. Junmei et al,
1999
HC-CT-C -O 1 0.08 180.0 3. Junmei et al,
1999

Such that the wild card:

X -C -CT-X 6 0.00 0.0 2. JCC,7,(1986),230

gets included and then the prmtop that leap spits out is:

...
       6: 0.800 0.00 1.0 :1_at_HH33 :1_at_CH3 :1_at_C :1_at_O (4,2,5,6)
E 7: 0.080 3.14 3.0 :1_at_HH33 :1_at_CH3 :1_at_C :1_at_O (4,2,5,6)
...
       9: 0.800 0.00 1.0 :1_at_HH32 :1_at_CH3 :1_at_C :1_at_O (3,2,5,6)
E 10: 0.000 0.00 2.0 :1_at_HH32 :1_at_CH3 :1_at_C :1_at_O (3,2,5,6)
E 11: 0.080 3.14 3.0 :1_at_HH32 :1_at_CH3 :1_at_C :1_at_O (3,2,5,6)
...
      14: 0.800 0.00 1.0 :1_at_HH31 :1_at_CH3 :1_at_C :1_at_O (1,2,5,6)
E 15: 0.000 0.00 2.0 :1_at_HH31 :1_at_CH3 :1_at_C :1_at_O (1,2,5,6)
E 16: 0.080 3.14 3.0 :1_at_HH31 :1_at_CH3 :1_at_C :1_at_O (1,2,5,6)
...
Total = 24 torsions...

So an interesting bug that doesn't seem to have ever been identified or
fixed - perhaps Wei can take a look at this and comment.

Personally my opinion is that there should be no wildcards in the force
field files. They are too ambiguous. As it stands though this bug is
innocuous but only because the wildcard barrier height is zero.

My introduction of the explicit value for HC-CT-C-O was to override this
torsion (and side step this bug) such that I could do some fitting whereby I
varied the barrier height for this torsion.

In the meantime I'll update the parm99.dat file for the next release so the
use of -ve periodicities is at least consistent.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Gregersen, Brent
> Sent: Friday, March 06, 2009 2:44 PM
> To: amber_at_ambermd.org
> Subject: [AMBER] Help with torsions in parm99.dat file
>
> Can anyone comment on the following torsion parameters (found in
> parm99.dat in at least amber 8-10):
>
> HC-CT-C -O 1 0.80 0.0 -1. Junmei et
> al, 1999
> HC-CT-C -O 1 0.08 180.0 3. Junmei et
> al, 1999
> HC-CT-C -O 1 0.00 0.0 2. Explicit of
> wild card X-C-CT-X
>
> The question I have regards the last line. Is it intended that this
> parameter overwrites the previous two? Or should it be included with the
> two above parameters (in which case the "3" should be "-3"). Also, why
> is it even necessary to list an explicit parameter of zero when a
> torsion for the 4 atom types already exists?
>
> I believe leap just ignores this parameter (or includes it with the
> previous two torsions), but from the documentation on the param.dat
> files http://ambermd.org/formats.html#parm.dat its not clear what the
> behaviour should be in this case.
>
> Thanks,
> Brent
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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