<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div>Hi everyone,<br><br>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;<br><br>"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..<br>-------------------------------------------------------------------------------------------------------<br>Back Off! I just backed up micelle_3.top to ./#micelle_3.top.2#<br>Processing chain 1 'A' (380 atoms, 10 residues)<br>There are 0 donors and 0 acceptors<br>There are 0 hydrogen bonds<br>Checking for duplicate atoms....<br>Opening library file /usr/local/gromacs/share/gromacs/top/specbond.dat<br>5 out of 5 lines of specbond.dat converted succesfully<br>No N- or C-terminus found: this chain appears to contain no protein<br>Now there are 10 residues with 380 atoms<br>Chain time...<br><br>Back Off! I just backed up micelle_3_A.itp to ./#micelle_3_A.itp.1#<br>Making bonds...<br>Opening library file
/usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>Number of bonds was 370, now 370<br>Generating angles, dihedrals and pairs...<br>Before cleaning: 360 pairs<br>Before cleaning: 360 dihedrals<br>Keeping all generated dihedrals<br>There are 360 dihedrals, 0 impropers, 370 angles<br> 360 pairs, 370 bonds and 0 virtual sites<br>Total mass 4643.948 a.m.u.<br>Total charge 0.000 e<br>Writing topology<br><br>Back Off! I just backed up posre_A.itp to ./#posre_A.itp.1#<br>Processing chain 2 'B' (2700 atoms, 1 residues)<br>There are 0 donors and 0 acceptors<br>There are 0 hydrogen bonds<br><span style="color: rgb(255, 0, 0);">Checking for duplicate atoms....</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">Now there are 27 atoms. Deleted 2673 duplicates.</span><br>Opening library file
/usr/local/gromacs/share/gromacs/top/specbond.dat<br>5 out of 5 lines of specbond.dat converted succesfully<br>No N- or C-terminus found: this chain appears to contain no protein<br>Now there are 1 residues with 27 atoms<br>Chain time...<br><br>Back Off! I just backed up micelle_3_B.itp to ./#micelle_3_B.itp.1#<br>Making bonds...<br>Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>Number of bonds was 27, now 27<br>Generating angles, dihedrals and pairs...<br>Before cleaning: 34 pairs<br>Before cleaning: 39 dihedrals<br>Keeping all generated dihedrals<br>There are 39 dihedrals, 0 impropers, 32 angles<br> 34 pairs, 27 bonds and 0 virtual sites<br>Total mass 315.218 a.m.u.<br>Total charge -0.000 e<br>Writing topology<br><br>Back Off! I just backed up posre_B.itp to
./#posre_B.itp.1#<br>Including chain 1 in system: 380 atoms 10 residues<br>Including chain 2 in system: 27 atoms 1 residues<br>Now there are 407 atoms and 11 residues<br>Total mass in system 4959.166 a.m.u.<br>Total charge in system 0.000 e<br><br>Writing coordinate file...<br><br>Back Off! I just backed up micelle_3.pdb to ./#micelle_3.pdb.1#<br> --------- PLEASE NOTE ------------<br>You have succesfully generated a topology from: mixed_sphere.pdb.<br>The oplsaa force field and the spc water model are used.<br>Note that the default mechanism for selecting a force fields has<br>changed, starting from GROMACS version 3.2.0<br> --------- ETON ESAELP ------------<br><br></div></div><br>
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