Hi there,
Thanks for the last reply, sorry.... i made a mistakes when writing previous
mail. I ran several tests, that's why the output is micelle_3.top and not
micelle_1 like i state in the command. If my pdb2gmx command was right
(regardless what file name for .gro and .top i put ) , and the structure i get
from the PRODRG (for surfactant and oil) is good (i've checked), why the
pdb2gmx program deleted the duplicates for surfactant and not for oil? Is there
any specifications for the pdb2gmx program to delete duplicates? These
duplicates generated using packmol software. Is that the problem? by the way,
the .top file referred to the .itp file correctly. Suggestions, ideas, and
advices are greatly appreciated. Thanks a lot :)
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