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.
-Justin
Thank you very much
Best regards
Meisam
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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