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-- 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/ | > > Note: Electronic Mail is not secure, has no guarantee of delivery, may not > be read every day, and should not be used for urgent or sensitive issues. > > > > > > _______________________________________________ > AMBER-Developers mailing list > AMBER-Developers.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber-developers > _______________________________________________ AMBER-Developers mailing list AMBER-Developers.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber-developersReceived on Mon Feb 08 2010 - 08:00:02 PST