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

Semen Esilevsky yesint4 at yahoo.com
Tue Jan 6 10:46:01 CET 2004

> 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.

I also think that this common task should be
implemented, but I can't find it... Probably somebody
know how to do it effectively - it's really tiring to
shift the coordinates with the Perl script.
> > 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.

Sure, I did energy minimization first and it ran
without problems. But after that I always have this
"30 deg" warning in the unrestrained run...
> 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!

The topology is correct. I did flavone in vacuum and
flavone in water - it's Ok.
As far as I know "30 deg" warning is mostly due to the
polar molecule (water?) trapped in the non-polar
region, but I don't have water in the membrane! Any suggestions?

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