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Bug #6

genbox remove protein from system

Added by junmin-quan empty almost 14 years ago. Updated almost 14 years ago.

Status:
Closed
Priority:
High
Assignee:
Erik Lindahl
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

genbox cp CD81-dimer.gro -cs spc216.gro -p CD81-dimer.top -o CD81-dimer
b4em.gro
:-) G R O M A C S (-:

Grunge ROck MAChoS
:-)  VERSION 3.3_rc1  (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, 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.
:-)  genbox  (-:

Option Filename Type Description
------------------------------------------------------------
-cp CD81-dimer.gro Input, Opt! Generic structure: gro g96 pdb tpr tpb tpa
xml
-cs spc216.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 CD81-dimer-b4em.gro Output Generic structure: gro g96 pdb xml
-p CD81-dimer.top In/Out, Opt! Topology file

Option   Type  Value  Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-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

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/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/top/atommass.dat
Opening library file /usr/local/gromacs/share/top/vdwradii.dat
Opening library file /usr/local/gromacs/share/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Reading solute configuration
?
Containing 1770 atoms in 180 residues
Initialising van der waals distances...
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 3x4x4 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 10368 residues
Calculating Overlap...
box_margin = 0.315
Removed 6309 atoms that were outside the box
Segmentation fault

History

#1 Updated by Erik Lindahl almost 14 years ago

This bug seems to have been fixed as a side-effect of the QM group bug David
corrected in the TPR format.

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