VMD-L Mailing List

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sun Oct 28 2007 - 05:23:11 CDT

Dear All,

Can VMD display force field atom types ?

If I take the Tripos mol2 file provided below:
In the @<TRIPOS>ATOM section, the 2nd column contains the atom names
and the 6th column contains the FF atom types.

If I go in VMD/Graphics/Colors, the colors of the "name" and "type" do
not differ...

Does it mean that the type color do not correspond to the force field
atom types ?

In these conditions, how to display the force field atom types ?
I am interested in force field atom types and not in "Type" from the
Type category.

Thanks, regards, Francois

@<TRIPOS>MOLECULE
AIB
    13 12 1 0 1
SMALL
USER_CHARGES
@<TRIPOS>ATOM
   1 N 1.090789 0.303623 -0.604732 N 1 AIB -0.4157
   2 H 1.583234 0.729459 -1.358031 H 1 AIB 0.2719
   3 CA -0.094215 1.027093 -0.131617 CT 1 AIB 0.1256
   4 CB1 -0.553574 1.932854 -1.284846 CT 1 AIB -0.2449
   5 HB11 0.210513 2.670857 -1.512912 HC 1 AIB 0.0798
   6 HB12 -0.758709 1.355295 -2.179624 HC 1 AIB 0.0798
   7 HB13 -1.455922 2.458623 -1.001371 HC 1 AIB 0.0798
   8 CB2 0.222110 1.873608 1.105707 CT 1 AIB -0.2449
   9 HB21 -0.650933 2.433115 1.408952 HC 1 AIB 0.0798
  10 HB22 0.530582 1.250582 1.932827 HC 1 AIB 0.0798
  11 HB23 1.022615 2.568960 0.869892 HC 1 AIB 0.0798
  12 C -1.268994 0.078289 0.171729 C 1 AIB 0.5973
  13 O -2.126839 0.412279 0.942507 O 1 AIB -0.5679
@<TRIPOS>BOND
     1 1 2 1
     2 1 3 1
     3 3 4 1
     4 3 8 1
     5 3 12 1
     6 4 5 1
     7 4 6 1
     8 4 7 1
     9 8 9 1
    10 8 10 1
    11 8 11 1
    12 12 13 1
@<TRIPOS>SUBSTRUCTURE
       1 AIB 1 **** 0 **** ****