VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Oct 28 2007 - 10:25:28 CDT

Hi Francois,
VMD is indeed displaying the force field type when you choose to color
by Type, but it treats the types the same was as it does atom names, in
that coloring for name and type is being done by the first letter of the
name and type (so that your HB11 and HB12 atoms don't get different
colors). If you'd like to change the colors used for types, you can edit
them in the Graphics->Colors menu. I'm not aware of a way to add new
type definitions currently; if you need to distinguish between types
(for example) "C" and "CT" (without changing one of them to something
like "TC"), for now you probably need to write a value to the beta field
based on the types, or display type labels for the atoms using something
like

set sel [atomselect top all]
foreach type [$sel get type] xyz [$sel get {x y z}] {
    graphics top text $xyz "$type"
}

If you do change the CT atoms to type TC, you should see a different
color show up, verifying that the type field is what is being used for
coloring, but again, I know that probably isn't terribly helpful ;-)

Peter

FyD wrote:
> 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 **** ****
>
>