[gmx-users] how to avoid pdb2gmx from deleting duplicates?

Alif M Latif prism_dead at yahoo.com
Wed May 23 09:55:42 CEST 2007

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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