README.txt
Update: July 2025  
Reference:  
  J. Min; M. Britt; B. R. Brooks; S. Sukharev; J. B. Klauda;  
  "Thermodynamics of arginine interactions with organic phosphates",  
  Biophysical Journal 124, 2176–2194 (2025).

----------------------------------------------------------------------------
Description
----------------------------------------------------------------------------
This update introduces new parameters for **arginine–organic phosphate 
interactions** based on the publication above. The main changes include:

1. **New NBFIX term**
   - Added for NC2 (guanidinium nitrogen of Arg) – O2L (phosphate oxygen)
   - Improves agreement with arginine–phosphate binding thermodynamics.

2. **New atom type: O2M**
   - Represents monoester phosphate oxygen (=O).
   - Introduced to prevent unintended effects of the NC2–O2L NBFIX.
   -------------------------------------------------------------------------
   O2L vs O2M
   -------------------------------------------------------------------------
   - **O2L**: original phosphate oxygen; subject to the new NC2–O2L NBFIX.  
   - **O2M**: chemically identical to O2L, but excluded from NC2–O2L NBFIX;  
     used only for monoester phosphates (e.g., phosphatidic acid).
   -------------------------------------------------------------------------

3. **Residue topology updates**  
   - Several residues in lipid topology/stream files have O2L atoms 
     replaced with O2M to ensure compatibility with the new parameters.  
   
   **Affected files/residues include:**
   - 'toppar_all36_lipid_model.str'  
     RESI MP_1, MP_2, PDAG  
   - 'toppar_all36_lipid_yeast.str'  
     RESI YOPA  
   - 'top_all36_lipid.rtf'  
     RESI DLPA, DMPA, DPPA, DSPA, DOPA, POPA  
   - 'toppar_all36_lipid_miscellaneous.str'  
     RESI PAPA, PSPA, DGPA, DEPA, DNPA, SLPA, PLPA, SAPA, SDPA, SOPA,  
          DAPA, DYPA, DIPA, TIPA, DTPA, LLPA, PLePA  
----------------------------------------------------------------------------


(1)
NBFIX
! new NBFix between NC2 and O2L
!                                        Emin         Rmin
!                                   (kcal/mol)     (A)

NC2     O2L    -0.1549    3.405

(2)
./top_all36_lipid.rtf:MASS  -1  O2M       15.99940 O ! =O in monoester phosphate groups
./par_all36_lipid.prm:MASS  -1  O2M       15.99940 ! =O in monoester phosphate groups
./par_all36_lipid.prm:O2M   PL    580.0       1.48    ! mono-ester phosphate; jmin, 07/25
./par_all36_lipid.prm:OSL  PL   O2M    98.9      111.6    ! mono-ester phosphate; jmin, 07/25
./par_all36_lipid.prm:OSLP PL   O2M    98.9      111.6    ! mono-ester phosphate; jmin, 07/25
./par_all36_lipid.prm:O2M  PL   O2M   120.0      120.0    ! mono-ester phosphate; jmin, 07/25
./par_all36_lipid.prm:O2M  PL   OHL    98.9      108.23   ! mono-ester phosphate; jmin, 07/25
./par_all36_lipid.prm:O2M  PL   OSLP CTL2     0.10    3     0.00 ! mono-ester phosphate; jmin, 07/25
./par_all36_lipid.prm:O2M  PL   OSL  CTL2     0.10    3     0.00 ! mono-ester phosphate; jmin, 07/25
./par_all36_lipid.prm:O2M  PL   OSLP CTL1     0.10    3     0.00 ! mono-ester phosphate; jmin, 07/25
./par_all36_lipid.prm:O2M  PL   OSL  CTL1     0.10    3     0.00 ! mono-ester phosphate; jmin, 07/25
./par_all36_lipid.prm:O2M  PL   OSLP CTL3     0.10    3     0.00 ! mono-ester phosphate; jmin, 07/25
./par_all36_lipid.prm:O2M  PL   OSL  CTL3     0.10    3     0.00 ! mono-ester phosphate; jmin, 07/25
./par_all36_lipid.prm:O2M      0.0       -0.12      1.70   ! mono-ester phosphate; jmin, 07/25
./toppar_water_ions.str:SOD    O2M      -0.07502    3.16  ! mono-ester phosphate; jmin, 07/25
./toppar_water_ions.str:CAL    O2M      -0.12       3.256 ! mono-ester phosphate; jmin, 07/25

(3)
./toppar_all36_lipid_model.str:155724: RESI MP_1 GROUP ! :: ATOM O3   TYPE O2L     <-- change to O2M
./toppar_all36_lipid_model.str:155725: RESI MP_1 GROUP ! :: ATOM O4   TYPE O2L     <-- change to O2M
./toppar_all36_lipid_model.str:155748: RESI MP_2 GROUP ! :: ATOM O2   TYPE O2L     <-- change to O2M
./toppar_all36_lipid_model.str:155749: RESI MP_2 GROUP ! :: ATOM O3   TYPE O2L     <-- change to O2M
./toppar_all36_lipid_model.str:155750: RESI MP_2 GROUP ! :: ATOM O4   TYPE O2L     <-- change to O2M
./toppar_all36_lipid_model.str:157234: RESI PDAG GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_model.str:157235: RESI PDAG GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_yeast.str:165030: RESI YOPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_yeast.str:165031: RESI YOPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./top_all36_lipid.rtf:223276: RESI DLPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./top_all36_lipid.rtf:223277: RESI DLPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./top_all36_lipid.rtf:224732: RESI DMPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./top_all36_lipid.rtf:224733: RESI DMPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./top_all36_lipid.rtf:226348: RESI DPPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./top_all36_lipid.rtf:226349: RESI DPPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./top_all36_lipid.rtf:228123: RESI DSPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./top_all36_lipid.rtf:228124: RESI DSPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./top_all36_lipid.rtf:229936: RESI DOPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./top_all36_lipid.rtf:229937: RESI DOPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./top_all36_lipid.rtf:231703: RESI POPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./top_all36_lipid.rtf:231704: RESI POPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:516665: RESI PAPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:516666: RESI PAPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:518425: RESI PSPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:518426: RESI PSPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:521474: RESI DGPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:521475: RESI DGPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:523500: RESI DEPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:523501: RESI DEPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:525686: RESI DNPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:525687: RESI DNPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:527645: RESI SLPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:527646: RESI SLPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:529364: RESI PLPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:529365: RESI PLPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:531831: RESI SAPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:531832: RESI SAPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:533288: RESI SDPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:533289: RESI SDPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:534730: RESI SOPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:534731: RESI SOPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:536156: RESI DAPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:536157: RESI DAPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:537193: RESI DYPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:537194: RESI DYPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:537817: RESI DIPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:537818: RESI DIPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:538490: RESI TIPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:538491: RESI TIPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:538793: RESI DTPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:538794: RESI DTPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:540137: RESI LLPA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:540138: RESI LLPA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:541836: RESI PLePA GROUP ! :: ATOM O13  TYPE O2L     <-- change to O2M
./toppar_all36_lipid_miscellaneous.str:541837: RESI PLePA GROUP ! :: ATOM O14  TYPE O2L     <-- change to O2M


