[gmx-users] Inserting small molecule into the solvated system

[Anton Feenstra]

Semen Esilevsky wrote:

> Dear Gromacs users,
> I've did equilibration of the pure membrane in water
> and now I have to add a small flavone probe to see how
> it incorporates into the membrane. 
> There are two problems:
> 
> 1) How to position the probe. I did it with the
> script, which shifts the coordinates aned then merge 
> pdb files but I suspect that it's possible to do it
> visually. Is it possible with Rasmol or VMD or
> something else?

Not with rasmol, that is only a viewer. It should be possible
with vmd, althouth I don't use it myself - so I'm not sure.

> 2) I have to delete several water molecules to make a
> hole for the probe. Doing this by hand always lead to
> LINKS warning about more than 30 deg rotation. I tried
> to delete all water and run genbox agin, but with the
> same warning. Then sumulation crashed on step 0.

Have you minimized before md? That is normally always
necessary whtn you change somthing in the coordinates.

You mention a flavone probe. You probably made a topology
for that yourself (or used one from Prodrg)? Can you minimize
that in vacuum, and if yes, can you do some md with it in
vacuum? If not, there is probably an error in the topology!

> What is a correct way to do the thing?

;-)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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