VMD-L Mailing List
From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sun Oct 28 2007 - 05:23:11 CDT
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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 **** ****
- Next message: Per Jr. Greisen: "Re: rna topology and parameters for rna"
- Previous message: Samuel Flores: "rna topology and parameters for rna"
- In reply to: John Stone: "Re: how to display dcd file written with catdcd using an index file"
- Next in thread: Peter Freddolino: "Re: Force field atom types"
- Reply: Peter Freddolino: "Re: Force field atom types"
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