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00readme_2020_release.txt
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00readme_2020_release.txt
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Overview of the 2020 polarizable Drude oscillator force field release.
May 2020
General comments
----------------
2020b - Atomtypes from 2020a were merged.
2020a - General updating of 2019 Drude toppar files to include
recent updates of parameters and unification of the atom
types and parameters across all the toppar files as
described below.
- Includes changes in parameters without
merging the atomtypes OD2C2C, OD30BN and PD1AN with
OD2C2B, OD30B and PD1A respectively.
## master file and proteins
toppar_drude_master_protein_2020b.str
---------------
* Merged PD1AN with PD1A, OD2C2C with OD2C2B, and OD30BN
with OD30B. Kept OD30BR for RNA specific bb dihedrals.
* Updated bonds, angles and dihedrals to comply with merge
* Updated the NBFIX and NBTHOLE according to merge
* File format edits by Ase.
* RESI LSN and PRES NNEU updated according to PAM1 and MAM1,
respectively. PRES GNNU added specific to GLY neutral N-termial.
* PRES HS2 updated according to update in HSE.
* Removed commented parameters (Hui-v9)
* From lipid, moved parameters for model compounds EAS, MPRO, etc
to allow using toppar_model without reading toppar_lipid.
toppar_drude_master_protein_2020a.str
---------------
* From toppar_drude_master_protein_2019g.str
* Major change was anionic compound nonbonded parameter update
(Molecular anions paper reference below)
PD1AN -- reverted back to PD1A
OD2C2B -- re-optimized
OD2C2C -- re-optimized
OD30BN -- reverted back to OD30B
OD30BR -- reverted back to OD30B
* Added atomtype SD1A for sulfur containing model compounds
* Moved NMA to model toppar file
* Added bonds, angles and dihedrals related to sulfur
containing model compounds
toppar_drude_d_aminoacids_2020b.str:
---------------
* No changes
toppar_drude_d_aminoacids_2020a.str:
---------------
* No changes
this is based on toppar_drude_d_aminoacids_2019g.str
## model compounds
toppar_drude_model_2020b.str
---------------
* Moved DMPN to DMP.
* Merged PD1AN with PD1A, OD2C2C with OD2C2B, and OD30BN
with OD30B.
* file format edits by Ase.
toppar_drude_model_2020a.str
---------------
* From toppar_drude_model_2019g.str
* Updated parameters and addtional compounds base
on anionic parameter update (see above) including:
Updated DMPN topology according to new DMP.
Updated methylphosphates MP_0, MP_1 and MP_2.
Added inorganic phosphates HP_1 and HP_2.
Added SO4, MSO4, MSNA, NMSM, NESM, MEO, ETO.
Ref: Kognole, A.A.; Aytenfisu, A.A.; MacKerell, A.D. Jr, "Balanced
Drude Polarizable Force Field Parameters for Molecular Anions:
Phosphates, Sulfates, Sulfamates and Oxides", Journal of
Molecular Modeling, (Just Accepted - April 2020)
## carbohydrates
toppar_drude_carbohydrate_2020b.str
---------------
* No change from 2020a
toppar_drude_carbohydrate_2020a.str
---------------
* From toppar_drude_carbohydrate_2019a.str
* No changes from 2019a
## The nucleic acid and lipid toppar files are not included
## with current 2020 release as the changes below based on recent
## developments have not been validated. As of May 2020
## additional optimization of the nucleic acid parameters was
## ongoing.
lipid
toppar_drude_lipid_2020b.str
---------------
* Removed DMPL
* Dihedral parameters for phosphate group were moved to
master following the atom type merger.
* Moved parameters for model compounds EAS, MPRO, MBU etc to
master to allow using model without reading lipid toppar.
toppar_drude_lipid_2020a.str
---------------
* From toppar_drude_lipid_2017c.str
* Updated DMPL and all the lipid topologies for the phosphate
groups according to the new DMP.
* Updated dihedral parameters for phosphodiester group
according to new optimized DMP.
- CD33C OD30B PD1A OD2C2B
- CD33C OD30B PD1A OD30B
## nucleic_acids
toppar_drude_nucleic_acid_2020b.str
---------------
* Merged PD1AN with PD1A, OD2C2C with OD2C2B, and OD30BN
with OD30B. Kept OD30BR for RNA specific phosphodiester
backbone dihedrals.
* Updated bonds, angles and dihedrals to comply with merge
* Updated the NBFIX and NBTHOLE according to merge
* File format edits by Ase.
* Updated PRES 3POM and 5POM according to new DMP.
toppar_drude_nucleic_acid_2020a.str
---------------
* From toppar_drude_nucleic_acid_2017c.str
* All nucleic acid residues containing a phosphodiester group
were updated for atom charges based on new DMP.
* All nucleobases (including methylated) were updated for
their alpha and thole parameters according to optimized
values to reduce the hardwall encounter issue.
* Updated the optimized backbone dihedrals for NA.
- epsilon and zeta optimized for BI:BII sampling in DNA.
- chi optimized for syn and anti.