Hi,

I met this problem that when I load a mol2 file into Jmol, the atoms named as CA was treated as calcium while I want it to be treated as carbon.
the file content is like this :
@<TRIPOS>MOLECULE
*****
 19 18 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
      1   CA        2.5480   -0.6650   -0.0320 C.3     0  _NS0       -0.0003
      2  HA1        2.4580   -1.2420   -0.9510 H       0  _NS0        0.0847
      3  HA2        2.5090   -1.3420    0.8220 H       0  _NS0        0.0847
      4    N        3.9060   -0.0150   -0.0200 N.4     0  _NS0        0.2209
      5  HT1        4.6470   -0.7050   -0.1970 H       0  _NS0        0.1995
      6  HT2        4.1170    0.4070    0.8910 H       0  _NS0        0.1995
      7  HT3        3.9960    0.6970   -0.7540 H       0  _NS0        0.1995
      8   C4        1.4690    0.4060    0.0670 C.3     0  _NS0        0.1322
      9  HC1        1.5610    0.9960    0.9830 H       0  _NS0        0.0752
     10  HC2        1.4920    1.0810   -0.7940 H       0  _NS0        0.0752
     11  O11        0.2260   -0.3190    0.0860 O.3     0  _NS0       -0.4560
     12  CA1       -0.8970    0.4310    0.0050 C.2     0  _NS0        0.3357
     13  O15       -0.9070    1.6370   -0.0990 O.2     0  _NS0       -0.2453
     14   C1       -2.1220   -0.4160    0.0630 C.2     0  _NS0        0.0418
     15  C15       -2.0380   -1.7160    0.2220 C.2     0  _NS0        0.0011
     16   C6       -3.4780    0.2620   -0.0570 C.3     0  _NS0       -0.0323
     17  H61       -4.2930   -0.4650   -0.0230 H       0  _NS0        0.0280
     18  H62       -3.5240    0.8040   -1.0070 H       0  _NS0        0.0280
     19  H63       -3.6000    0.9730    0.7660 H       0  _NS0        0.0280
@<TRIPOS>BOND
     1     1     2    1
     2     1     3    1
     3     1     4    1
     4     1     8    1
     5     4     5    1
     6     4     6    1
     7     4     7    1
     8     8     9    1
     9     8    10    1
    10     8    11    1
    11    11    12    1
    12    12    13    2
    13    12    14    1
    14    14    15    2
    15    14    16    1
    16    16    17    1
    17    16    18    1
    18    16    19    1

The result from that is the atom CA and CA1 are painted as two large green calcium. I googled it and saw people mentioned set atomTypes. But it didn't work for me. The script would set up the atomType. However the interpretation of the atom is  no based on this type(field 6 in the mol2 file), but on the name of the atom (field 2). That causes for the ambiguity of CA as C or Calcium.

Anyway, anyone know how to solve it?

Cheers,