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

Semen Esilevsky yesint4 at yahoo.com
Fri Jan 2 13:19:01 CET 2004

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?

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.

What is a correct way to do the thing?

--- David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> On Thu, 1 Jan 2004, Byungchan Kim wrote:
> >Hi Folks.
> >
> >I want to calculate S2 order parameter with
> g_rotacf.
> >>From mailing list discussion, I could figure out
> how to use g_rotacf on my
> >purpose. My command is like this,
> >g_rotacf -f 4pti.trj.xtc -n NH_21.ndx -d -P 2
> >NH_21.ndx is like this
> >[NH_21]
> >329     333
> >
> >My problem is that I couldn't get the flat value of
> correlation function.
> >The simulation lasted up to 1.5 ns.
> >What I am curious about is whether the program use
> orientation of
> >interatomic vector "in molecular frame". Actually,
> I am not sure it is a
> >problem if the program does not use the molecular
> frame.
> >I am looking forward to hearing clever answer.
> g_rotacf does not use the moleuclar frame. You can
> try to run the 
> trajectory through trjconv first, fitting everyhting
> to reference 
> structure (and only outputting the protein) and then
> run g_rotacf.
> >
> >Thank you very much and Happy New Year.
> >Byungchan
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
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> >Please don't post (un)subscribe requests to the
> list. Use the 
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> >
> -- 
> David.
> David van der Spoel, PhD, Assist. Prof., Molecular
> Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala
> University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org  
> http://xray.bmc.uu.se/~spoel
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