######Partial charges calculation protocol######


######ASH and ASM######

partial charges from oplsaa force field 


######PNPP and PNP -> determined in vacuo at HF/6-31G(d)######

##GAUSSIAN OPTIMIZATION AND ELECTROSTATIC POTENTIAL

##Gaussian modules

Gaussian/16.C.01-avx2-nsc1-bdist

##Optimization and Electrostatic Potential

HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt  (input)

##RESP CHARGES WITH ANTECHAMBER

##Amber modules

buildtool-easybuild/4.5.0-nscabf0c8c  ifort/.2018.1.163-GCC-6.4.0-2.28  impi/.2018.1.163
Amber/16-AmberTools-17-patchlevel-8-12-nsc1

##Run Antechamber on the output from gaussian

antechamber -fi gout -fo prepi -c resp -i hf.log -o name.in -rn NAME -at amber -pf y


#######CYM and CSP (negative and phosphorylated cysteine)######

##GAUSSIAN OPTIMIZATION AND ELECTROSTATIC POTENTIAL

##Gaussian modules

Gaussian/16.C.01-avx2-nsc1-bdist

##1a. Add cap residues ACE and NME

##Optimization with MP2/6-31G*

opt mp2/6-31g(d) scrf=cpcm (input)

##Calculate Electrostatic Potential

P HF/6-31G* SCF=Tight Pop=MK IOp(6/33=2) (input)

##RESP CHARGES WITH ANTECHAMBER

##Amber modules

buildtool-easybuild/4.5.0-nscabf0c8c  ifort/.2018.1.163-GCC-6.4.0-2.28  impi/.2018.1.163
Amber/16-AmberTools-17-patchlevel-8-12-nsc1

##Run Antechamber on the output from gaussian

antechamber -fi gout -fo prepi -c resp -i hf.log -o name.in -rn NAME -at amber -pf y



#####RESULTS#####

######PND
HF/6-31G(d) + RESP - SI
N      NO2            0.796300 
ON1    ON            -0.552900 
ON2    ON            -0.552900 
CG     CA            -0.133800 
CD1    CA            -0.124400 
CD2    CA            -0.124400 
CE1    CA            -0.441600 
CE2    CA            -0.441600 
CZ     CA             0.905000 
OH     OHP           -0.712300 
HE2    HA             0.186300 
HE1    HA             0.186300 
HD1    HA             0.169400 
HD2    HA             0.169400 
PO     PO             1.386200 
OP1    O2Z           -0.905000 
OP2    O2Z           -0.905000 
OP3    O2Z           -0.905000 

######PNP
HF/6-31G(d) opt + RESP                          
N      NO2            0.791765                 
ON1    ON            -0.473331                  
ON2    ON            -0.473331                   
CG     CA            -0.013840                   
CD1    CA            -0.128552                  
CD2    CA            -0.128552                   
CE1    CA            -0.307112
CE2    CA            -0.307112
CZ     CA             0.426797                   
OH     OTY           -0.530959  
HE2    HA             0.189633 
HE1    HA             0.189633 
HD1    HA             0.188340 
HD2    HA             0.188340 
HH     HO             0.388281

######CYM and SS1
mp2-6-31gd opt + resp fitting + rescale using "q_rescale" (backbone charges changed to be consisted with oplsaa charges)          
 
N      N             -0.500000 #  -0.500000 (dq=+0.000000)                                          
H      H              0.300000 #   0.300000 (dq=+0.000000)                                          
CA     CT             0.140000 #   0.140000 (dq=+0.000000)                                          
HA     HC             0.060000 #   0.060000 (dq=+0.000000)                                          
CB     CT            -0.275578 #  -0.246468 (dq=-0.029110)                                          
HB2    HC             0.111416 #   0.126338 (dq=-0.014922)                                          
HB3    HC             0.111416 #   0.126338 (dq=-0.014922)                                          
SG     SG            -0.947254 #  -0.847193 (dq=-0.100061)                                          
C      C              0.500000 #   0.500000 (dq=+0.000000)                                          
O      O             -0.500000 #  -0.500000 (dq=+0.000000)                                          


######CSP
mp2-6-31gd opt + resp fitting + rescale using "q_rescale" (backbone charges changed to be consisted with oplsaa charges)
N      N             -0.500000 #  -0.500000 (dq=+0.000000)                                                                                         
HN     HC             0.300000 #   0.300000 (dq=+0.000000)                                                                                   
CA     CT             0.140000 #   0.140000 (dq=+0.000000)                                                                                      
HA     HC             0.060000 #   0.060000 (dq=+0.000000)                                                                                         
CB     CT            -0.177147 #  -0.171224 (dq=-0.005923)                                                                                       
HB2    HC             0.107859 #   0.111724 (dq=-0.003865)                                                                                      
HB3    HC             0.107859 #   0.111724 (dq=-0.003865)                                                                                    
S      SG            -0.499064 #  -0.482377 (dq=-0.016687)                                                                                   
P      PO             1.133997 #   1.174630 (dq=-0.040633)                                                                                
O1     O2Z           -0.891168 #  -0.861370 (dq=-0.029798)                                                                                      
O2     O2Z           -0.891168 #  -0.861370 (dq=-0.029798)                                                                                   
O3     O2Z           -0.891168 #  -0.861370 (dq=-0.029798)                                                               
C      C              0.500000 #   0.500000 (dq=+0.000000)                                                                                       
O      O             -0.500000 #  -0.500000 (dq=+0.000000)                                                                                       


