Re: [AMBER-Developers] SCEE and SCNB removed

From: Lachele Foley <lfoley.ccrc.uga.edu>
Date: Mon, 08 Feb 2010 10:52:01 -0500

> 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.

I'm willing to try, too. It seems appropriate since this is so relevant to our group. But, I'm a total leap-code-noob and probably shouldn't promise anyone anything right now. I can take a peek, tho, and see how painful it looks if there isn't anyone better available.


:-) Lachele
--
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
706-542-0263
lfoley.ccrc.uga.edu
----- Original Message -----
From: Ross Walker
[mailto:ross.rosswalker.co.uk]
To: 'AMBER Developers Mailing List'
[mailto:amber-developers.ambermd.org]
Sent: Mon, 08 Feb 2010 09:43:22
-0500
Subject: [AMBER-Developers] SCEE and SCNB removed
> 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:
> 
> %FLAG SCEE_SCALE_FACTOR
> %FORMAT(5E16.8)
>   1.20000000E+00  1.30000000E+00  1.00000000E+00  1.70000000E+00
> 1.20000000E+00
>   1.20000000E+00  1.30000000E+00
> %FLAG SCNB_SCALE_FACTOR
> %FORMAT(5E16.8)
>   2.00000000E+00  2.10000000E+00  1.00000000E+00  1.00000000E+00
> 2.10000000E+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
> 2.0.
> 
> 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
> 
> becomes:
> 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:
> 
> DIHE
> 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
> 
> 14NONBOND
> 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
> default.
> 
> 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
> Ross
> 
> /\
> \/
> |\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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> 
> 
> 
> 
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