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.
Mark
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