Dear All..
i want to add octanol as solvent...bt everytime i give genbox command it says
0 solvent molecules added.
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.
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
:-) G R O M A C S (-:
Gnomes, ROck Monsters And Chili Sauce
:-) VERSION 3.3.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2006, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) /usr/local/gromacs/bin/genbox (-:
Option Filename Type Description
------------------------------------------------------------
-cp kif1g_md_box_oct.gro Input, Opt! Generic structure: gro g96 pdb tpr
tpb tpa xml
-cs octanol512.gro Input, Opt!, Lib. Generic structure: gro g96 pdb tpr tpb
tpa xml
-ci insert.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
xml
-o kif1g_md_oct.gro Output Generic structure: gro g96 pdb xml
-p kif1g.top In/Out, Opt! Topology file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 19 Set the nicelevel
-box vector 0 0 0 box size
-nmol int 0 no of extra molecules to insert
-try int 10 try inserting -nmol*-try times
-seed int 1997 random generator seed
-vdwd real 0.105 default vdwaals distance
-shell real 0 thickness of optional water layer around solute
-maxsol int 0 maximum number of solvent molecules to add if
they fit in the box. If zero (default) this is
ignored
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
In case you use free energy of solvation predictions:
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. Eisenberg and A. D. McLachlan
Solvation energy in protein folding and binding
Nature 319 (1986) pp. 199-203
-------- -------- --- Thank You --- -------- --------
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Reading solute configuration
DRG
Containing 68 atoms in 1 residues
Initialising van der waals distances...
Reading solvent configuration
"OcOH Pure Solvent"
solvent configuration contains 13824 atoms in 512 residues
Initialising van der waals distances...
Will generate new solvent configuration of 1x1x1 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
OcOH ( 27 atoms): 512 residues
Calculating Overlap...
box_margin = 0.45
Removed 7155 atoms that were outside the box
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45
System total charge: 0.000
Grid: 17 x 17 x 17 cells
Succesfully made neighbourlist
nri = 23737, nrj = 792271
Checking Protein-Solvent overlap: tested 941 pairs, removed 378 atoms.
Checking Solvent-Solvent overlap: tested 32848 pairs, removed 2187 atoms.
Added 152 molecules
Generated solvent containing 4104 atoms in 152 residues
Writing generated configuration to kif1g_md_oct.gro
Back Off! I just backed up kif1g_md_oct.gro to ./#kif1g_md_oct.gro.2#
DRG
Output configuration contains 4172 atoms in 153 residues
Volume : 58.7777 (nm^3)
Density : 541.15 (g/l)
Number of SOL molecules: 0
Please guide...wheres the problem....
Regards
nur
---------------------------------
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