Dear All..<br> i want to add octanol as solvent...bt everytime i give genbox command it says 0 solvent molecules added.<br> I got the octanol equilibrated box from gromacs contributors section. it was of ffooplsa type...when i changed the atom types and topology through prodrg...the same problem persists.<br> <br> bash-3.00# /usr/local/gromacs/bin/genbox -cp kif1g_md_box_oct.gro -cs octanol512.gro -o kif1g_md_oct.gro -p kif1g.top<br> :-) G R O M A C S (-:<br> <br> Gnomes, ROck Monsters And Chili Sauce<br> <br>
:-) VERSION 3.3.1 (-:<br> <br> <br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br> Copyright (c) 2001-2006, The GROMACS development team,<br> check out http://www.gromacs.org for more information.<br> <br> This program is free software; you can redistribute it and/or<br> modify it under the terms of the GNU General Public License<br> as published by
the Free Software Foundation; either version 2<br> of the License, or (at your option) any later version.<br> <br> :-) /usr/local/gromacs/bin/genbox (-:<br> <br> Option Filename Type Description<br> ------------------------------------------------------------<br> -cp kif1g_md_box_oct.gro Input, Opt! Generic structure: gro g96 pdb tpr<br> tpb tpa xml<br> -cs octanol512.gro Input, Opt!, Lib. Generic structure: gro g96 pdb tpr tpb<br>
tpa xml<br> -ci insert.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa<br> xml<br> -o kif1g_md_oct.gro Output Generic structure: gro g96 pdb xml<br> -p kif1g.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 0 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/local/gromacs/share/gromacs/top/aminoacids.dat<br> Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat<br> Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat<br> Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat<br> #Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7<br> Reading solute configuration<br> DRG<br> Containing 68 atoms in 1 residues<br> Initialising van der waals distances...<br> Reading solvent configuration<br> "OcOH Pure Solvent"<br> solvent configuration contains 13824 atoms in 512 residues<br> <br> Initialising van der waals distances...<br> Will generate new solvent configuration of 1x1x1 boxes<br> Generating configuration<br> Sorting configuration<br> Found 1 molecule type:<br> OcOH ( 27 atoms): 512 residues<br> Calculating Overlap...<br> box_margin = 0.45<br>
Removed 7155 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> Grid: 17 x 17 x 17 cells<br> Succesfully made neighbourlist<br> nri = 23737, nrj = 792271<br> Checking Protein-Solvent overlap: tested 941 pairs, removed 378 atoms.<br> Checking Solvent-Solvent overlap: tested 32848 pairs, removed 2187 atoms.<br> Added 152 molecules<br> Generated solvent containing 4104 atoms in 152 residues<br> Writing generated configuration to kif1g_md_oct.gro<br> <br> Back Off! I just backed up kif1g_md_oct.gro to ./#kif1g_md_oct.gro.2#<br> DRG<br> <br> Output configuration contains 4172 atoms in 153 residues<br> Volume
: 58.7777 (nm^3)<br> Density : 541.15 (g/l)<br> <span style="font-weight: bold; text-decoration: underline;">Number of SOL molecules: 0</span><br> <br> Please guide...wheres the problem....<br> <br> Regards<br> nur<br> <p> 
        
        
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