van der Waals Radii

van der Waals Radii to Use with Connolly's MS

The file of radii and atom types supplied with the program, file2.dat, is not generally used in applications of the program. The table below list various radii sets along with an atom type numbering that can be used with the program for calculations with proteins and other bio- molecules. Some of these radii were optimized for particular purposes such as molecular mechanics energy calculations. Thus, they should be used cautiously for other purposes.

NOTE: the first column does not list values for all atom types because unambiguous documentation of the contents of the file2.dat file was not found.

                                  QCPE   Biosym  Bondi  Bondi  Tannor et                              Rashin et
Radii:                             MS      MS     1964  1968   al. (1994) Amber 4.1 CHARMm 2.2  MM3   al. (1994)
Purpose**                        MS Demo   MS     Gen.   Gen.    Delphi    vdW en.   vdW en.   vdW en.   dHel
Atom Atom   Description
1     C2    CH2 group             1.53    1.90    1.7    2.0      1.9       1.908     1.8       2.04     2.46
2     C3    CH3 group             1.53    1.95    1.7    2.0      1.9       1.908     1.8       2.04     2.46
3     CO    Aldehyde C            1.53    1.80    1.7    1.74     1.9       1.908*    1.87      1.94     2.46
4     COa   Carboxylic/amide C    1.53    1.80    1.7    1.74     1.9       1.908     1.87      1.94     2.46
5     CH    Aromatic CH group     1.53    1.90    1.77   1.77     1.99      1.908     2.04      1.96     2.46
6     Car   Aromatic C (no H)     1.53    1.80    1.77   1.77     1.99      1.908     2.04      1.96     2.46
	
10    OH    Hydroxyl O            1.36    1.70    1.52   1.45     1.6       1.721     1.55      1.82     1.5
11    OHp   Phenolic OH           1.36    1.70    1.52*  1.45     1.6       1.721     1.55      1.82     1.5
12    OHa   Carboxylic OH         1.36    1.60    1.52*  1.45     1.6       1.721     1.55      1.82     1.5
13    OC    Aldehyde O            1.36    1.60    1.5    1.65     1.6       1.6612    1.54      1.82     1.5
14    OCa   Carboxylic carbonyl   1.36    1.60    1.5    1.50     1.6       1.6612    1.66      1.82     1.5
15    OCo   COOH carbonyl O       1.36    1.60    1.5*   1.50     1.6       1.6612    1.52      1.82     1.5
16    OCq   Quinone C=O                           1.5    1.65     1.6       1.6612    1.55      1.82     1.5
17    ON    Nitro O                               1.53   1.50     1.6       1.6612*   1.66*     1.82*    1.5
18    OP    Phosphate O                   1.64    1.5*   1.50               1.6612
19    OS    Sugar, Nucleic acid O         1.40	

20    NH    Amine N               1.45    1.70    1.55   1.7      1.6       1.824     1.65      1.93     1.5
21    NH+   Protonated Amine N    1.45    1.75    1.55*           1.6       1.824     1.65      1.93     1.5
22    NA    Amide N               1.45    1.65    1.55*  1.7      1.6       1.824     1.83      1.93     1.5
23    Ng    Guanidinium Group N   1.50            1.55*  1.55               1.824
24    Nn    Nucleotide aromatic N         1.55    1.55*  1.6                1.824
25    NO    Nitro N                       1.65    1.55   1.55     1.6       1.824     1.83*     1.93     1.5

30    PO    Phosphate P                   1.80    1.80                      2.1       1.9       2.2
32    SO    Sulfate S                             1.75            1.9       2.0       1.89      2.15*
33    SH    Thiol & thioether S   1.70    1.90    1.80   1.8      1.9       2.0       1.89      2.15*
34    OW    TIP3P water O                                                   1.7683    1.768     
35    HW    TIP3P water H                                                   0.0
36    HT    TIPS3P water H                                                            0.92

40    H1    CHO, aldehyde H               1.20    1.2*            1.15      1.409     1.33      1.62     1.71
41    H2    CH2, H atom                   1.20    1.2             1.15      1.487     1.33      1.62     1.71
42    H3    CH3, H atom                   1.20    1.2             1.15      1.487     1.33      1.62     1.71
43    HC    Aromatic CH, H                1.20    1.0             1.36      1.459     1.33      1.62     1.71
44    HCN   HC-N+                         1.20    1.2             1.15      1.387     1.33      1.62     1.71
45    HO    Hydroxyl/phenolic H           1.20    0.6*            1.15      0.0       0.76      1.60     1.16
46    HOa   Carboxylic OH                 1.20    0.6*            1.15      0.0       0.80      0.90     1.16
47    HN    Amine H                       1.20    0.6*            1.15      0.6       0.80      1.60     1.16
48    HN+   Protonated amine H            1.20    0.6*            1.15      0.6       0.60      1.60     1.16
49    HNa   Amide H                       1.20    0.6             1.15      0.6       0.80      1.60     1.16

** Purposes: vdW = van der Waals, MM = molecular mechanics, en.= MM energy component, MS = molecular surface calculation,
             Delphi = Delphi electrostatic energy calculation, dHel = radii used in electrostatic enthalpy calculation
* Assigned for this table, but not explicitly defined or assigned by the author. Asterisks are left off when the data set 
  has no subclassification (i.e. all values the same for a give atom).