/usr/share/gromacs/top/dgsolv.dat is in gromacs-data 4.5.5-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 | ;
; Atomic solvation parameters: i.e. free energy of solvation (kcal/mol) per
; unit of solvent exposed area (A^2). The atomnames are really atomtypes!
;
; Data from Eisenberg and McLachlan, Nature 319 (1986), 199-203
; These numbers are for united atoms.
;
; Read this only using the function get_dgsolv (include "atomprop.h")
;
??? C 0.016
??? N -0.006
??? O -0.006
; In the original paper by Eisenberg and McLachlan, GLU and ASP sidechains
; have one negative oxygen atom (OM) and normal (O). The OM is then selected
; to be the most solvent accessible one. Since in a simulation
; such sidechains will usually flip around anyway we average the constants
; here, so OM' = (OM + O)/2
;??? OM -0.024
??? OM -0.015
??? NL -0.050
??? S 0.021
??? H 0.0
; Right now the data from the ref below are *not* used!
; Data are taken from Wang et al. J Phys Chem B 105 (2001) p 5055-5067
; to be more precise this is from table 4, model 4
;
;??? C3 0.0117970
;??? C2 -0.0183314
;??? C1 -0.4449764
;??? CT 0.0697875
;??? CA -0.0480703
;??? CD2 -0.1236206
;??? CD1 -0.1226437
;??? CD 0.0246029
;??? CS -0.0061025
;??? CO -0.1178312
;??? CN 0.0208413
;??? F 0.0194227
;??? Cl -0.0015111
;??? Br -0.0068335
;??? I -0.0066410
;??? HCT3 -0.0061394
;??? HCT2 -0.0365374
;??? HC -0.0365374
;??? HCT1 -0.0215288
;??? HCT 0.0062124
;??? HCD2 0.1459805
;??? HCD1 0.0820232
;??? HCD 0.1036663
;??? HCA 0.0220654
;??? HCS 0.0100682
;??? HO -0.0029297
;??? HN -0.2363502
;??? HS 0.0377756
;??? OA -0.3006240
;??? OC -0.0816844
;??? O -0.1357120
;??? OS 0.1176048
;??? OOH -0.1421025
;??? SH -0.0372476
;??? SS -0.0121603
;??? SP -0.0477491
;??? NS -0.1143369
;??? ND2 -0.3270664
;??? ND3 -0.4072273
;??? NO 0.7646976
;??? NH2 0.5234891
;??? NH1 -0.3474580
;??? N -0.4713683
;??? NTH2 0.2720645
;??? NTH 0.0325122
;??? NT -0.3476829
;??? P3 1.5160293
;??? P4 -0.2509340
;??? O- -1.2154901
;??? OA- -2.1887474
;??? S- -1.1141940
;??? HN+ -1.3254553
;??? NT+ 6.2614711
;??? ND+ -5.7053672
;??? N+ 2.6350040
|