[AMBER-Developers] SCEE and SCNB removed

From: Ross Walker <ross.rosswalker.co.uk>
Date: Mon, 8 Feb 2010 06:43:22 -0800

Hi All,

Following up on what Dave suggested at the AMBER meeting I have removed SCNB
and SCEE from the namelist. I have checked this change into the tree and I
believe updated all the test cases to match. It is possible that I missed
some though so please let me know if you see any problems.

As the code stands right now it will look in the prmtop file for the
following sections:

  1.20000000E+00 1.30000000E+00 1.00000000E+00 1.70000000E+00
  1.20000000E+00 1.30000000E+00
  2.00000000E+00 2.10000000E+00 1.00000000E+00 1.00000000E+00
  2.30000000E+00 2.30000000E+00

These should have NDIHEDRALS types entries. If it finds these sections it
will use these for the 1-4 scaling. So for Glycam for example these would be
1.0 for all entries here. For glycam mixed with ff99SB all glycam dihedral
types would be 1.0, all ff99SB dihedral types would be 1.2 and 2.0
respectively and all mixed glycam ff99SB dihedral types would be 1.2 and

If the code does not find these sections in the prmtop it defaults to 1.2
and 2.0 for scee and scnb. This means that right now if you want to run
glycam or the original weiner etc al force fields then you either need to
modify the code to change the defaults or make sure these entries are in
your prmtop. Thus we should probably update x,y,zleap to write these
sections based on entires in the prmtop. Volunteers? I know gleap (and I
assume sleap) can already do this although there is not any documentation on
how to turn this on.

I propose we update the parmxx.dat file as follows:

O2-S -N -H 1 -0.10 0.0 6. ***G06 - MT
O2-S -N -CG 1 0.11 0.0 -3. ***G06 - MT
              1 0.00 0.0 -2.
              1 0.00 0.0 1.
S -N -CG-H1 1 0.02 0.0 3. ***G06 - MT

O2-S -N -H 1 -0.10 0.0 6. ***G06 - MT
O2-S -N -CG 1 0.11 0.0 -3. ***G06 - MT
              1 0.00 0.0 -2.
              1 0.00 0.0 1.
S -N -CG-H1 1 0.02 0.0 3. ***G06 - MT

O2-S -N -H 1.2 2.0
O2-S -N -CG 1.2 2.0
S -N -CG-H1 1.2 2.0

A frcmod file would then be:

O2-S -N -H 1 -0.10 0.0 6. ***G06 - MT
O2-S -N -CG 1 0.11 0.0 -3. ***G06 - MT
              1 0.00 0.0 -2.
              1 0.00 0.0 1.
S -N -CG-H1 1 0.02 0.0 3. ***G06 - MT

O2-S -N -H 1.2 2.0
O2-S -N -CG 1.2 2.0
S -N -CG-H1 1.2 2.0

The idea here being that this SCEE/SCNB entry is NOT mandatory meaning it
remains backwards compatible. If it is not found then the default of 1.2 /
2.0 is simply used. If we modify leap to always write the entries in the
prmtop file then we could simply have a

set default SCEE 1.2

option in leap, with the default being 1.2. This would allow pure GLYCAM /
Weiner et al sims to be run by just setting these defaults to 1.0 in when
building the prmtop in leap. Then any dihedral terms explicitly specifying
SCEE and SCNB values found in parmxx.dat or frcmod would override this

The issue right now is how to modify the various leaps to include the code
for reading these extra values, and also writing the extra prmtop sections.
Do we have anyone 'nominated' to maintain such things in x,t,s,gleap? Can we
coordinate this change? I can try to do it myself but it might take a while
for me to work out how to do it.

Comments? Suggestions for doing this better? Leap gurus who think they could
implement this easily?

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |

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Received on Mon Feb 08 2010 - 07:00:03 PST
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