[gmx-users] Re: gmx-users Digest, Vol 90, Issue 48

meisam valizadeh kiamahalleh meisam488 at gmail.com
Wed Oct 12 20:28:00 CEST 2011

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
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?
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 water.
> >  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 specific
> > 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
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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