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? 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
> 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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