[gmx-users] Surfactant molecules missing after genbox

Mark Abraham Mark.Abraham at anu.edu.au
Wed May 23 09:15:34 CEST 2007

Alif M Latif wrote:
> Hi everyone,
> Firstly thanks to Stephane for replying my mail. I've checked the memory 
> and solve the problem. unfortunately, there's another problem.. After i 
> minimize the micelle structure using steepest descent , I ran MD. But 
> when I observed the trajectory, there's only one surfactant molecule 
> left on the structure ( supposed to be 100 !!)

Right, so here's a lesson. Check your structure visually at each step to 
see that it is what you think it should be!

> There supposed to be 20 
> oil structure, 100 surfactant plus spc water from genbox. When i look 
> back, the surfactants started missing after i converted the .pdb file to 
> .top and .gro file using pdb2gmx. I built the structure using Packmol. 
> The output .pdb file from the  packmol program looks fine. I wonder how 
> this happened. I use this command for pdb2gmx;
> "pdb2gmx -f micelle_1.pdb -o micelle_1.gro -p micelle_1.top" There were 
> no warning at all, making me more confused. I found that the program 
> deleted the duplicated surfactants. Why the program didn't delete the 
> oil's duplicates?. The surfactants pdb file i got from PRODRG webserver. 
> Can some body give me any idea? Thanks a lot..
> -------------------------------------------------------------------------------------------------------
> Back Off! I just backed up micelle_3.top to ./#micelle_3.top.2#

Here's your first clue... your actual command was writing micelle_3.top, 
not micelle_1.top as you imply above.

> Processing chain 1 'A' (380 atoms, 10 residues)
> There are 0 donors and 0 acceptors
> There are 0 hydrogen bonds
> Checking for duplicate atoms....
> Opening library file /usr/local/gromacs/share/gromacs/top/specbond.dat
> 5 out of 5 lines of specbond.dat converted succesfully
> No N- or C-terminus found: this chain appears to contain no protein
> Now there are 10 residues with 380 atoms
> Chain time...
> Back Off! I just backed up micelle_3_A.itp to ./#micelle_3_A.itp.1#

Is your .top file referring to these .itp files for different 
moleculetypes correctly? Check manual chapter 5 for info here - and an 
example with urea, IIRC.


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