Dear GMXusers,<br> I wanna insert several silicon atoms into an ice crystal. I use genbox with a Silicon.pdb, but there's no any silicon atom in the out file. Do I miss anything? Anyone has some comments? Thanks a lot.<br>
<br>Best,<br>william<br><br><br> Here's output log:<br><br>root@xwei:~/Desktop/gromacs/icesi# genbox -cp ice.pdb -ci Si.pdb -o icesi.pdb -nmol 10<br> <br>Option Filename Type Description<br>
------------------------------------------------------------<br> -cp ice.pdb Input, Opt! Generic structure: gro g96 pdb tpr tpb tpa<br> xml<br> -cs spc216.gro Input, Opt., Lib. Generic structure: gro g96 pdb tpr tpb<br>
tpa xml<br> -ci Si.pdb Input, Opt! Generic structure: gro g96 pdb tpr tpb tpa<br> xml<br> -o icesi.pdb Output Generic structure: gro g96 pdb xml<br>
-p topol.top In/Out, Opt. Topology file<br><br> Option Type Value Description<br>------------------------------------------------------<br> -[no]h bool no Print help info and quit<br> -[no]X bool no Use dialog box GUI to edit command line options<br>
-nice int 19 Set the nicelevel<br> -box vector 0 0 0 box size<br> -nmol int 10 no of extra molecules to insert<br> -try int 10 try inserting -nmol*-try times<br> -seed int 1997 random generator seed<br>
-vdwd real 0.105 default vdwaals distance<br> -shell real 0 thickness of optional water layer around solute<br> -maxsol int 0 maximum number of solvent molecules to add if<br> they fit in the box. If zero (default) this is<br>
ignored<br><br>WARNING: masses will be determined based on residue and atom names,<br> this can deviate from the real mass of the atom type<br>In case you use free energy of solvation predictions:<br>
<br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>D. Eisenberg and A. D. McLachlan<br>Solvation energy in protein folding and binding<br>Nature 319 (1986) pp. 199-203<br>-------- -------- --- Thank You --- -------- --------<br>
<br>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 solute configuration<br>Gromacs Runs On Most of All Computer Systems<br>Containing 1080 atoms in 360 residues<br>Initialising van der waals distances...<br>
Reading molecule configuration <br><br>Containing 40 atoms in 1 residue<br>Initialising van der waals distances...<br>Try 15box_margin = 0.48<br>Removed 0 atoms that were outside the box<br>Neighborsearching with a cut-off of 0.48<br>
Table routines are used for coulomb: FALSE<br>Table routines are used for vdw: FALSE<br>Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48<br>System total charge: 0.000<br>Grid: 9 x 9 x 9 cells<br>nri = 2105, nrj = 25364<br>
Checking Protein-Solvent overlap: tested 20 pairs, removed 40 atoms.<br>Checking Solvent-Solvent overlap: tested 0 pairs, removed 0 atoms.<br>Try 99<br>Added 0 molecules (out of 10 requested) of <br>Writing generated configuration to icesi.pdb<br>
Gromacs Runs On Most of All Computer Systems<br><br>Output configuration contains 1080 atoms in 360 residues<br>Volume : 11.4017 (nm^3)<br>Density : 944.556 (g/l)<br>Number of SOL molecules: 360<br>