[gmx-users] problem regarding editconf - atommass
ARUN KUMAR
arun.target at gmail.com
Thu Nov 16 20:24:49 CET 2006
Hai all....
I am trying to simulate the bulk phase decane system using
GROMACS........... I used decane pdb file which I goT from HIC UP.... I
changed the residue name to C10 from D10 to match the residue name in
ffgmx.rtp(GROMACS force field)....
I ran pdb2gmx , selected forcefield "4"(ffgmx)... and got .top and gro files
for my decane molecule...There saw the molecule mass as 142.17 which is
correct ....... Now as I want to simulate Bulk I used genconf to get my 512
molecule system..... i got out.gro file from this..... To get the desired
density I used editconf to get 602 gr/ltr ....But here in out put as shown
below its showing the different mass for 512 molecules i.e 61498.9.....(see
output of editconf)......which means that single molecule mass is
120.11.......means hydrogen masses are missing....... I checked
atommass.datand I am unable to know what I have to do.....
Awaiting for help
Arun
GENCONF output
[arun at cluster ~]$ !genconf
genconf -nbox 8 8 8 -dist 1 1 1 -f conf.gro
:-) G R O M A C S (-:
GROup of MAchos and Cynical Suckers
:-) VERSION 3.2.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, 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.
:-) genconf (-:
Option Filename Type Description
------------------------------------------------------------
-f conf.gro Input Generic structure: gro g96 pdb tpr tpb tpa
xml
-o out.gro Output Generic structure: gro g96 pdb xml
-trj traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96
pdb
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 0 Set the nicelevel
-nbox vector 8 8 8 Number of boxes
-dist vector 1 1 1 Distance between boxes
-seed int 0 Random generator seed, if 0 generated from the
time
-[no]rot bool no Randomly rotate conformations
-[no]shuffle bool no Random shuffling of molecules
-[no]sort bool no Sort molecules on X coord
-block int 1 Divide the box in blocks on this number of cpus
-nmolat int 3 Number of atoms per molecule, assumed to start
from 0. If you set this wrong, it will screw up
your system!
-maxrot vector 90 90 90 Maximum random rotation
-[no]renumber bool no Renumber residues
gcq#77: "One Cross Each" (Monty Python)
###############################################################################
After then I ran editconf to change density .............. I used 512 decane
molecules... But I did not get the total mass of 512*142=72704 amu...
Instead I got 61498.9 which is 512*120 that means hydrogen masses are
missing.... Can anyone help me in this regard.........................
##############################################################
Here is the output................
[arun at cluster ~]$ editconf -density 602 -f out.gro
:-) G R O M A C S (-:
Gromacs Runs On Most of All Computer Systems
:-) VERSION 3.2.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, 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.
:-) editconf (-:
Option Filename Type Description
------------------------------------------------------------
-f out.gro Input Generic structure: gro g96 pdb tpr tpb tpa
xml
-n index.ndx Input, Opt. Index file
-o out.gro Output Generic structure: gro g96 pdb xml
-bf bfact.dat Input, Opt. Generic data 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 0 Set the nicelevel
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]ndef bool no Choose output from default index groups
-bt enum tric Box type for -box and -d: tric, cubic,
dodecahedron or octahedron
-box vector 0 0 0 Box vector lengths (a,b,c)
-angles vector 90 90 90 Angles between the box vectors (bc,ac,ab)
-d real 0 Distance between the solute and the box
-[no]c bool no Center molecule in box (implied by -box and -d)
-center vector 0 0 0 Coordinates of geometrical center
-translate vector 0 0 0 Translation
-rotate vector 0 0 0 Rotation around the X, Y and Z axes in degrees
-[no]princ bool no Orient molecule(s) along their principal axes
-scale vector 1 1 1 Scaling factor
-density real 602 Density (g/l) of the output box achieved by
scaling
-[no]vol bool yes Compute and print volume of the box
-[no]pbc bool no Remove the periodicity (make molecule whole
again)
-[no]mead bool no Store the charge of the atom in the occupancy
field and the radius of the atom in the B-factor
field
-[no]grasp bool no Store the charge of the atom in the B-factor
field and the radius of the atom in the
occupancy
field
-rvdw real 0.12 Default Van der Waals radius if one can not be
found in the database
-[no]atom bool no Force B-factor attachment per atom
-[no]legend bool no Make B-factor legend
-label string A Add chain label for all residues
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 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 /opt/gromacs-3.2.1/share/top/aminoacids.dat
Opening library file /opt/gromacs-3.2.1/share/top/atommass.dat
Opening library file /opt/gromacs-3.2.1/share/top/vdwradii.dat
Opening library file /opt/gromacs-3.2.1/share/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Read 5120 atoms
Volume: 1207.38 nm^3, corresponds to roughly 543300 electrons
No velocities found
system size : 16.008 7.874 7.000 (nm)
center : 8.504 4.437 4.000 (nm)
box vectors : 17.008 8.874 8.000 (nm)
box angles : 90.00 90.00 90.00 (degrees)
box volume :1207.38 (nm^3)
Volume of input 1207.38 (nm^3)
Mass of input 61498.9 (a.m.u.)
Density of input 84.5812 (g/l)
Scaling all box vectors by 0.519867
new system size : 8.322 4.093 3.639
new center : 4.421 2.307 2.079 (nm)
new box vectors : 8.842 4.613 4.159 (nm)
new box angles : 90.00 90.00 90.00 (degrees)
new box volume : 169.64 (nm^3)
Back Off! I just backed up out.gro to ./#out.gro.1#
gcq#267: "In the End Science Comes Down to Praying" (P. v.d. Berg)
--
Arun kumar.V
M.E Chemical
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