[PyMOL] bonds in ligands for MD simulations?

[vincent C. <vin...@ib...>]

Dear everyone,

I have a MD simulation of coarse grain molecules, therefore not defined 
as typically for "normal" protein/ligands, but as beads.
I want to represent it using Pymol, and need to define bonds between the 
beads.
The problem is that I have 400 copies of my ligand, and all with the 
same name. I want to link bead1 with bead2, all having the name LIG.
How can I do it?

The CONECT record works only to define connections on a one-on-one 
basis, so it would be horrible for the whole file.
I tried the bond command in pymol with the following argument, but it 
doesn't work:
PyMOL>bond resi LIG and name B1, resi LIG and name B2
Editor-Warning: bonds cannot be created between objects, only within.

I guess this command line will create also bonds between B1 to all the 
399 other LIG B2...
(If "resi" would take into account the residue number, it would work?)

here is what the pdb file looks like:

ATOM6129B1LIG97740.880 105.97099.0901.000.00
ATOM6130B2LIG97741.700 105.20097.1801.000.00
ATOM6131B3LIG97741.880 104.86094.7501.000.00
...
ATOM6138B1LIG978116.680 127.990 105.9901.000.00
ATOM6139B2LIG978117.300 129.230 107.7201.000.00
ATOM6140B3LIG978119.340 130.290 108.5901.000.00
...


thank you for your help.
best
Vincent



-- 

Vincent Chaptal, PhD

Institut de Biologie et Chimie des Protéines

Drug-resistance modulation and mechanism Laboratory

7 passage du Vercors

69007 LYON

FRANCE

+33 4 37 65 29 07

http://www.ibcp.fr