<div id="RTEContent"> Hi<br> I am new to GROMACS.<br> <br> I intend to do simulation with simple DNA.<br> After some manupulation of the original PDB file(with no water), I was able to run<br> pdb2gmx and editconf. After editconf, I tried genbox to solvate the DNA but I got error.<br> <br> Here is what I did<br> > <span style="text-decoration: underline;">pdb2gmx -missing -f 111.pdb -p 1.top -o 1.gro<br> <br> > editconf -f 1.gro -o nopbc -d 0.5 -bt dodecahedron -nopbc<br> <br> Everything is fine and no error so far. But when I tried the following..<br> <br> > genbox -cp nopbc.gro -cs spc216 -p -o nonopbc<br> .....<br> .....<br> .....<br> </span> <pre>Opening library file /usr/share/gromacs/top/aminoacids.dat<br>Opening library file /usr/share/gromacs/top/atommass.dat<br>Opening library file /usr/share/gromacs/top/vdwradii.dat<br>Opening library file /usr/share/gromacs/top/dgsolv.dat<br>#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat:
7<br>Reading<br> solute<br> configuration<br>GROwing Monsters And Cloning Shrimps<br>Containing 589 atoms in 28 residues<br>Initialising van der waals distances...<br>Reading solvent configuration<br>"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"<br>solvent configuration contains 648 atoms in 216 residues<br><br>Initialising van der waals distances...<br>Will generate new solvent configuration of 3x3x2 boxes<br>Generating configuration<br>Sorting configuration<br>Found 1 molecule type:<br> SOL ( 3 atoms): 3888 residues<br>Calculating Overlap...<br>box_margin = 0.315<br>Removed 2901 atoms that were outside the box<br>Neighborsearching with a cut-off of 0.45<br>Table routines are used for coulomb: FALSE<br>Table routines are used for vdw: FALSE<br>Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45<br>System total charge: 0.000<br>Neighborsearching with a cut-off of 0.45<br>Grid: 20 x 20 x 14 cells<br>Succesfully made neighbourlist<br>nri = 20651, nrj
=<br> 449052<br>Checking<br> Protein-Solvent overlap: tested 9501 pairs, removed 1134 atoms.<br>Checking Solvent-Solvent overlap: tested 87594 pairs, removed 1404 atoms.<br>Added 2075 molecules<br>Generated solvent containing 6225 atoms in 2075 residues<br>Writing generated configuration to nopbc_fin.gro<br><br>Back Off! I just backed up nopbc_fin.gro to ./#nopbc_fin.gro.3#<br>GROwing Monsters And Cloning Shrimps<br><br>Output configuration contains 6814 atoms in 2103 residues<br>Volume : 73.1608 (nm^3)<br>Density : 1043.86 (g/l)<br>Number of SOL molecules: 2075<br><br>Processing topology<br>-------------------------------------------------------<br>Program genbox, VERSION 3.3<br>Source code file: futil.c, line: 340<br><br>File input/output error:<br>topol.top<br>-------------------------------------------------------<br><br>"If You Want Something Done You Have to Do It Yourself" (Highlander II)</pre> <br> <br> In the end, I have no
topology file ! <br> Of course if I run genbox without -p option, genbox gives no error but I don't have topology file and I can not run simulation ( Well.. I suppose).<br> <br> So, what am I doing wrong ? This is my very first GOMACS trial.<br> Thank you<br> <br> Soo </div><p>
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