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

[Mark Abraham]

Alif M Latif wrote:
> 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 :)

Start a clean folder, do everything slowly and methodically, recording 
what you do as you go, and see where the problem first appears. If it 
looks like pdb2gmx is doing something inconsistent, you need to prove 
(at least to yourself) that it's not you doing something inconsistent. 
The first step there is knowing what you've done :-)

Mark