Hi Soo,<br><br>To start with, you have to supply the topology generated with pdb2gmx to genbox. The option -p defaults to topol.top, but you named your topology 1.top. Therefore genbox complains that there's no topol.top and you should give -p
1.top instead.<br><br>In addition, one thing struck me in your sequence of commands. You used pdb2gmx -missing. Why is that? Do you know what it does? It ignores missing atoms if they aren't listed in the pdb file. If atoms are indeed missing, it's a very good recipe for crashing a simulation. And why are you using editconf with the option -nopbc? That's pointless unless you hand topology information to editconf (a .tpr file) which it can use to make your molecule whole, in case it is broken. I would expect that the pdb file doesn't contain a broken molecule; it won't if it's from an experimentally determined structure or the direct result of a simulation with gromacs.
<br><br>Cheers,<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 12/14/05, <b class="gmail_sendername">Soo J</b> <<a href="mailto:icarustiki@yahoo.com">icarustiki@yahoo.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div> 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:<br> 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> =<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><span class="sg"> <br> Soo </span></div><span class="ad"><p>
</p><hr size="1">Yahoo! Shopping<br>
Find Great Deals on Holiday Gifts at <a href="http://us.rd.yahoo.com/mail_us/footer/shopping/*http://shopping.yahoo.com/;_ylc=X3oDMTE2bzVzaHJtBF9TAzk1OTQ5NjM2BHNlYwNtYWlsdGFnBHNsawNob2xpZGF5LTA1+%0A" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
Yahoo! Shopping</a>
<p></p></span><br>_______________________________________________<br>gmx-users mailing list<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org">
gmx-users-request@gromacs.org</a>.<br><br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry
<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>