[gmx-users] problem with genion (gromacs 3.3.99)
Julie Bernauer
bernauer at stanford.edu
Wed May 21 23:37:36 CEST 2008
Hi all,
I do have a weird behaviour with genion, which fails with the message:
ftp2fn: No filetype .???
No option -cpo
Segmentation fault
and I can't figure out what I do wrong. I couldn't not find any
reference to it either.
It seems that a file cannot be accessed but I couldn't get in what way.
As it works fine with gromacs 3.3, I don't really get what the problem
could be.
The details are below and I can provide other information / files if needed.
Thanks in advance for your help,
--
Julie
---------------
Here is what the problem look like:
$ my_genion -s 1bd8_em.tpr -o 1bd8_em.pdb -pname Na -np 4 -g genion.log
:-) G R O M A C S (-:
S C A M O R G
:-) VERSION 3.3.99_development_200800503 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, 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.
:-) my_genion (-:
Option Filename Type Description
------------------------------------------------------------
-s 1bd8_em.tpr Input Generic run input: tpr tpb tpa xml
-table table.xvg Input, Opt. xvgr/xmgr file
-n index.ndx Input, Opt. Index file
-o 1bd8_em.pdb Output Generic structure: gro g96 pdb xml
-g genion.log Output Log file
-pot pot.pdb Output, Opt. Protein data bank file
-p topol.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
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-np int 4 Number of positive ions
-pname string Na Name of the positive ion
-pq int 1 Charge of the positive ion
-nn int 0 Number of negative ions
-nname string Cl Name of the negative ion
-nq int -1 Charge of the negative ion
-rmin real 0.6 Minimum distance between ions
-[no]random bool yes Use random placement of ions instead of based on
potential. The rmin option should still work
-seed int 1993 Seed for random number generator
-scale real 0.001 Scaling factor for the potential for -pot
-conc real 0 Specify salt concentration (mol/liter). This
will
add sufficient ions to reach up to the
specified
concentration as computed from the volume
of the
cell in the input tpr file. Overrides the
-np and
nn options.
-[no]neutral bool no This option will add enough ions to neutralize
the system. In combination with the
concentration
option a neutral system at a given salt
concentration will be generated.
Back Off! I just backed up genion.log to ./#genion.log.8#
WARNING: turning of free energy, will use lambda=0
Reading file 1bd8_em.tpr, VERSION 3.3.99_development_200800503 (single
precision)
ftp2fn: No filetype .???
ftp2fn: No filetype .???
No option -cpo
Segmentation fault
------------
It seems to work well with the standard gromacs 3.3 though (same files,
only grompp redone):
genion -s 1bd8_em.tpr -o 1bd8_em.pdb -pname Na -np 4 -g genion.log
:-) G R O M A C S (-:
Gyas ROwers Mature At Cryogenic Speed
:-) VERSION 3.3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, 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.
:-) genion (-:
Option Filename Type Description
------------------------------------------------------------
-s 1bd8_em.tpr Input Generic run input: tpr tpb tpa xml
-table table.xvg Input, Opt. xvgr/xmgr file
-n index.ndx Input, Opt. Index file
-o 1bd8_em.pdb Output Generic structure: gro g96 pdb xml
-g genion.log Output Log file
-pot pot.pdb Output, Opt. Protein data bank file
-p topol.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
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-np int 4 Number of positive ions
-pname string Na Name of the positive ion
-pq int 1 Charge of the positive ion
-nn int 0 Number of negative ions
-nname string Cl Name of the negative ion
-nq int -1 Charge of the negative ion
-rmin real 0.6 Minimum distance between ions
-[no]random bool yes Use random placement of ions instead of based on
potential. The rmin option should still work
-seed int 1993 Seed for random number generator
-scale real 0.001 Scaling factor for the potential for -pot
-conc real 0 Specify salt concentration (mol/liter). This
will
add sufficient ions to reach up to the
specified
concentration as computed from the volume
of the
cell in the input tpr file. Overrides the
-np and
nn options.
-[no]neutral bool no This option will add enough ions to neutralize
the system. In combination with the
concentration
option a neutral system at a given salt
concentration will be generated.
Back Off! I just backed up genion.log to ./#genion.log.1#
WARNING: turning of free energy, will use lambda=0
Reading file 1bd8_em.tpr, VERSION 3.3.3 (single precision)
Using a coulomb cut-off of 1 nm
Will try to add 4 Na ions and 0 Cl ions.
Select a continuous group of solvent molecules
Opening library file /usr/share/gromacs/top/aminoacids.dat
Group 0 ( System) has 36644 elements
Group 1 ( Protein) has 2342 elements
Group 2 ( Protein-H) has 1168 elements
Group 3 ( C-alpha) has 156 elements
Group 4 ( Backbone) has 468 elements
Group 5 ( MainChain) has 625 elements
Group 6 (MainChain+Cb) has 766 elements
Group 7 ( MainChain+H) has 777 elements
Group 8 ( SideChain) has 1565 elements
Group 9 ( SideChain-H) has 543 elements
Group 10 ( Prot-Masses) has 2342 elements
Group 11 ( Non-Protein) has 34302 elements
Group 12 ( SOL) has 34302 elements
Group 13 ( Other) has 34302 elements
Select a group: 12
Selected 12: 'SOL'
Number of (3-atomic) solvent molecules: 11434
Replacing solvent molecule 1341 (atom 6365) with Na
Replacing solvent molecule 8663 (atom 28331) with Na
Replacing solvent molecule 5581 (atom 19085) with Na
Replacing solvent molecule 9673 (atom 31361) with Na
Back Off! I just backed up 1bd8_em.pdb to ./#1bd8_em.pdb.1#
gcq#122: "The Path Of the Righteous Man is Beset On All Sides With the
Iniquities Of the Selfish and the Tyranny Of Evil Men." (Pulp Fiction)
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