[gmx-users] Surfactant molecules missing after genbox

[Alif M Latif]

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 !!) 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#
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#
Making bonds...
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Number of bonds was 370, now 370
Generating angles, dihedrals and pairs...
Before cleaning: 360 pairs
Before cleaning: 360 dihedrals
Keeping all generated dihedrals
There are  360 dihedrals,    0 impropers,  370 angles
           360 pairs,      370 bonds and     0 virtual sites
Total mass 4643.948 a.m.u.
Total charge 0.000 e
Writing topology

Back Off! I just backed up posre_A.itp to ./#posre_A.itp.1#
Processing chain 2 'B' (2700 atoms, 1 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Checking for duplicate atoms....
Now there are 27 atoms. Deleted 2673 duplicates.
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 1 residues with 27 atoms
Chain time...

Back Off! I just backed up micelle_3_B.itp to ./#micelle_3_B.itp.1#
Making bonds...
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Number of bonds was 27, now 27
Generating angles, dihedrals and pairs...
Before cleaning: 34 pairs
Before cleaning: 39 dihedrals
Keeping all generated dihedrals
There are   39 dihedrals,    0 impropers,   32 angles
            34 pairs,       27 bonds and     0 virtual sites
Total mass 315.218 a.m.u.
Total charge -0.000 e
Writing topology

Back Off! I just backed up posre_B.itp to ./#posre_B.itp.1#
Including chain 1 in system: 380 atoms 10 residues
Including chain 2 in system: 27 atoms 1 residues
Now there are 407 atoms and 11 residues
Total mass in system 4959.166 a.m.u.
Total charge in system 0.000 e

Writing coordinate file...

Back Off! I just backed up micelle_3.pdb to ./#micelle_3.pdb.1#
                --------- PLEASE NOTE ------------
You have succesfully generated a topology from: mixed_sphere.pdb.
The oplsaa force field and the spc water model are used.
Note that the default mechanism for selecting a force fields has
changed, starting from GROMACS version 3.2.0
                --------- ETON ESAELP ------------





       
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