* Atomic radius derived from solvent electrostatic charge distribution
* Tested with free energy perturbation with explicit solvent
* Authors: Mafalda Nina, Dmitrii Belogv, and Benoit Roux
* University of Montreal, June 1996.
* M. Nina and B. Roux. Atomic Radii for Continuum Electrostatics Calculations based on
* Molecular Dynamics Free Energy Simulations. J. Phys. Chem. B 101: 5239-5248 (1997).
*
! For pHMD on Asp and Glu we need to ensure that the added protons are in the anti position.
! The code below rebuilds all of the Asp and Glu protons and places them in the anti (180 degrees)
! position. The assumption in this bit of code is that all Asp and Glu residues should be acted on
! AND that the patches used to make ASPP2 and GLUP2 have had the ICs added for the HD/HE dihedrals
coor init select ( resname glu .or. resname asp ) .and. ( type hd* .or. type he* ) end
ic build
prnlev 0 ! Turn off printing here
! UPDATES:
! --------
! 1. PMF guided optimization of input radii for charged residues (2005)
! ref: J. Chen, W. Im and C. L. Brooks III, JACS (submitted).
!
!
! GLU and ASP modified December 1st, 1998 by Mafalda Nina
!
! Protonated histidine HSP has been included, January 1999 by Mafalda Nina
! dG_elec = -68.15 kcal/mol (MD/FES) or -68.10 kcal/mol (PBEQ)
!
! TEA and ions added by Benoit Roux, January 1999.
!
! sodium added by Benoit Roux, November 2000
scalar wmain set 1.3 select type ZN end
! Set to zero all H radii
scalar wmain set 0.0 sele chem H* end
! Set heavy atoms to average default values
scalar wmain set 2.3 sele chem C* end
scalar wmain set 1.8 sele chem O* end
scalar wmain set 2.3 sele chem N* end
scalar wmain set 2.3 sele chem S* end
!Patches CT3 N-Methylamide C-terminus
!ACE acetylated N-terminus (ACP for PRO)
scalar wmain set 2.06 sele (type CAY .or. type CAT) end
scalar wmain set 2.04 sele type CY end
scalar wmain set 1.52 sele type OY end
scalar wmain set 2.23 sele type NT end
scalar wmain set 1.40 sele type OT* end ! for COO- terminus
!Backbone
scalar wmain set 2.04 sele type C end
! for peptide bond
scalar wmain set 1.52 sele type O end
! for peptide bond
scalar wmain set 2.23 sele type N end
! for peptide bond
scalar wmain set 2.86 sele type CA end
! for all CA except GLY
scalar wmain set 2.38 sele (resnam GLY .and. type CA) end
! for GLY only
!Hydrogens
scalar wmain set 0.00 sele type H* end
! for all hydrogens
!Carbons
scalar wmain set 2.67 sele type CB end
! for all residues
scalar wmain set 2.46 sele type CG* end
! for ARG, GLN, ILE, LYS, MET, PHE, THR, TRP, VAL, HSP, HSD
scalar wmain set 2.77 sele resnam GLU .and. type CG end
! for GLU only
scalar wmain set 2.44 sele type CD* end
! for ARG, ILE, LEU, LYS
scalar wmain set 1.98 sele (resnam GLN .and. type CD) .or. (resnam ASN .and. type CG) .or. -
(resnam GLU .and. type CD) .or. (resnam ASP .and. type CG) end
! for ASP, GLU, ASN, GLN
scalar wmain set 1.98 sele (resnam PRO .and. (type CB .or. type CG .or. type CD)) end
! for PRO only
scalar wmain set 2.00 sele (resnam TYR .and. (type CE* .or. type CD* .or. -
type CZ)) .or. (resnam PHE .and. (type CE* .or. -
type CD* .or. type CZ)) end
! for TYR, PHE rings
scalar wmain set 1.78 sele (resnam TRP .and. (type CE* .or. type CD* .or. -
type CZ* .or. type CH2)) end
! for TRP ring only
scalar wmain set 2.10 sele type CE end
! for MET only
scalar wmain set 2.80 sele (resnam ARG .and. type CZ) .or. (resnam LYS .and. type CE) end
! for ARG, LYS
scalar wmain set 1.98 select (( resnam HSD .or. resnam HSP .or. resn HIS ) .and. type CE1) -
.or. (( resnam HSD .or. resnam HSP .or. resn HIS ) .and. type CD2) end
! for neutral HSD and protonated HSP
!Oxygens
scalar wmain set 1.40 sele (resnam GLU .or. resnam ASP) .and. (type OE* .or. type OD*) end
! for GLU, ASP
scalar wmain set 1.42 sele (resnam ASN .or. resnam GLN) .and. (type OE* .or. type OD*) end
! for ASN, GLN
scalar wmain set 1.64 sele type OG* end
! for SER, THR
scalar wmain set 1.85 sele (resnam TYR .and. type OH) end
! for TYR only
scalar wmain set 2.2 select resname TIP3 .and. type OH2 end
! for explicit water molecules
!Nitrogens
scalar wmain set 1.80 sele ( resn HSD .or. resn HIS ) .and. (type NE2 .or. type ND1) end
! for neutral HSD (HIS is HSD)
scalar wmain set 2.30 sele resnam HSP .and. (type NE2 .or. type ND1) end
! for protonated HSP
scalar wmain set 2.13 sele resnam ARG .and. (type NH* .or. type NE) .or. -
(resnam LYS .and. type NZ) end
! for ARG, LYS
scalar wmain set 2.15 sele (resnam GLN .and. type NE2) .or. (resnam ASN .and. type ND2) end
! for GLN, ASN
scalar wmain set 2.40 sele resnam TRP .and. type NE1 end
! for TRP
!Sulphur
scalar wmain set 2.00 sele type S* end
! for MET, CYS
!Ions
scalar wmain set 2.035 select resname POT end
!potassium ion K+
scalar wmain set 2.035 select resname CLA end
!chloride ion Cl-
scalar wmain set 1.66 select resname SOD end
!sodium ion Na+
scalar wmain set 2.15 sele resnam TEA .and. type N end
scalar wmain set 2.30 sele ( type C1 .or. type C2 .or. type C3 .or. type C4 ) .and. resnam TEA end
scalar wmain set 2.30 sele ( type C5 .or. type C6 .or. type C7 .or. type C8 ) .and. resnam TEA end
! Tetramethylamonium (TEA)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! PMF guided optimization of input radii for charged residues !!
!! !!
!! J. Chen, W. Im and C. L. Brooks III, JACS (submitted) !!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! NOTE: should be used only with GBSW;
!! NOTE: for optimal accuracy in peptide and protein conformational equilibrium,
!! the modified CMAP in "~toppar/gbsw/par_all22_prot_gbsw.inp" should be used.
!!
! ASP and GLU (no change)
! LYS:
scalar wmain set 1.8 select resn LYS .and. type NZ end
! ARG:
scalar wmain set 1.7 select resn ARG .and. ( type NH* .or. type NE ) end
scalar wmain set 2.2 select resn ARG .and. type CZ end
! GLN and ASN
scalar wmain set 1.6 select resn GLN .and. type OE1 end
scalar wmain set 1.6 select resn ASN .and. type OD1 end
scalar wmain set 2.0 select resn GLN .and. type NE2 end
scalar wmain set 2.0 select resn ASN .and. type ND2 end
! HSD and HSP: hnd(1.8->1.9), hpnd/hpne(2.3->1.9)
scalar wmain set 1.9 select resn HSD .and. type ND1 end
scalar wmain set 1.9 select resn HSD .and. type NE2 end
scalar wmain set 1.9 select resn HSP .and. type ND1 end
scalar wmain set 1.9 select resn HSP .and. type NE2 end
! TRP: NE (2.4->1.8), C*(1.78->2.0)
scalar wmain set 1.85 select resn TRP .and. type NE1 end
scalar wmain set 2.0 select resn TRP -
.and. (type CE* .or. type CD* .or. type CZ* .or. type CH2) end
! backbone (bb6)
scalar wmain set 2.03 sele type N end !2.23
scalar wmain set 2.03 sele type NL .or. type NR end ! alad
! terminus
scalar wmain set 2.03 sele type NT end ! 2.23
scalar wmain set 2.77 sele type CGY end ! from GLU CG
scalar wmain set 2.67 sele type CAY end ! from CB
scalar wmain set 1.98 sele type CDY end ! from GLU CD
scalar wmain set 1.40 sele type OEY* end ! from GLU OE*
scalar wmain set 1.52 sele type OY end ! from backbone O
scalar wmain set 2.04 sele type CY endi ! from backbone C
prnlev 5 ! turn print level back on
gbsw reset
gbsw sgamma 0.005 nang 50 conc 0.15
