<div class="gmail_quote"><div>Dear Justin</div><div>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.</div>
<div>1) May I know if I should use the drug resname or molecule name infront of -nmol?</div><div>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?</div>
<div>Thank you very much</div><div>Best regards</div><div>Meisam</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">meisam valizadeh kiamahalleh wrote:<br>
> Dear GMX users<br>
> Good day to you<br>
> I have some drug molecules (cisplatin) added manually and<br>
> randomly inside a system which is going to be solvated in spc216 water.<br>
> I used genbox command to add the correct number of water molecules<br>
> needed to solvate the box. The drug molecules are located very closed to<br>
> each other. Kindly, would you please let me know how I can distribute<br>
> drug molecules uniformly among the water molecoules to obtain a<br>
> certain concentration of the drug? May I know if there is any specific<br>
> tool or script which can help me to do it?<br>
<br>
I don't know how you did the initial insertion, but genbox -ci -nmol will add<br>
molecules randomly, after which you can solvate with water. Don't combine these<br>
steps. Do the insertion, then add the water.<br>
<br>
-Justin<br>
<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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