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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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