[gmx-users] Uniform Distribution of drug molecules inside water spc216
Justin A. Lemkul
jalemkul at vt.edu
Wed Oct 12 20:30:50 CEST 2011
meisam valizadeh kiamahalleh wrote:
> Dear Justin
> Thank you very much for your always prompt reply. Actually, I added many
> of drug molecules by copying and pasting a single molecule in discovery
> studio software. I could even move the drug molecules to any desired
> locations by select and dragging them. Finally I used the output pdb
> file from discovery studio as initial structure in Gromacs, but I could
> not find any option for the molecule uniform distribution.
> 1) May I know if I should use the drug resname or molecule name infront
> of -nmol?
The -nmol option takes an integer argument. Please see genbox -h.
> 2) As you mention the method suggested by you would add the drug
> molecules randomly. then, May I also Know if they can
> be uniformly distributed in the water after solvation?
You can only build a random configuration with genbox -ci -nmol. If you want an
artificially crystalline system, use genconf -nbox to replicate your existing
drug molecule as many times as you'd like in whatever dimensions you want.
Either way, you'll have to do sufficient equilibration to get a homogeneous
system, if it's even possible. I'd think the latter approach would be worse
since you're starting from a very highly ordered system.
> Thank you very much
> Best regards
> meisam valizadeh kiamahalleh wrote:
> > Dear GMX users
> > Good day to you
> > I have some drug molecules (cisplatin) added manually and
> > randomly inside a system which is going to be solvated in spc216
> > I used genbox command to add the correct number of water molecules
> > needed to solvate the box. The drug molecules are located very
> closed to
> > each other. Kindly, would you please let me know how I can distribute
> > drug molecules uniformly among the water molecoules to obtain a
> > certain concentration of the drug? May I know if there is any
> > tool or script which can help me to do it?
> I don't know how you did the initial insertion, but genbox -ci -nmol
> will add
> molecules randomly, after which you can solvate with water. Don't
> combine these
> steps. Do the insertion, then add the water.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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