[gmx-users] Fwd: Umbrella sampling Tutorial Fatal Error

[Nima Soltani]

Excuse me that I forgot to attach the complete Error page:
nima at nima-ThinkPad:~/Desktop/3$ gmx grompp -f md_pull.mdp -c npt.gro -p
topol.top -n index.ndx -t npt.cpy -o pull.tpr
GROMACS:    gmx grompp, VERSION 5.0.2

GROMACS is written by:
Emile Apol         Rossen Apostolov   Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren  Rudi van Drunen    Anton Feenstra     Sebastian Fritsch
Gerrit Groenhof    Christoph Junghans Peter Kasson       Carsten Kutzner
Per Larsson        Justin A. Lemkul   Magnus Lundborg    Pieter Meulenhoff
Erik Marklund      Teemu Murtola      Szilard Pall       Sander Pronk
Roland Schulz      Alexey Shvetsov    Michael Shirts     Alfons Sijbers
Peter Tieleman     Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
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as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, VERSION 5.0.2
Executable:   /usr/local/gromacs/bin/gmx
Library dir:  /usr/local/gromacs/share/gromacs/top
Command line:
  gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpy
-o pull.tpr


NOTE 1 [file md_pull.mdp, line 62]:
  md_pull.mdp did not specify a value for the .mdp option "cutoff-scheme".
  Probably it was first intended for use with GROMACS before 4.6. In 4.6,
  the Verlet scheme was introduced, but the group scheme was still the
  default. The default is now the Verlet scheme, so you will observe
  different behaviour.

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'optimize_fft'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
ERROR: pull-coord1-groups should have 2 components

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#

WARNING 1 [file md_pull.mdp, line 62]:
  Unknown left-hand 'pull_group0' in parameter file



WARNING 2 [file md_pull.mdp, line 62]:
  Unknown left-hand 'pull_group1' in parameter file



WARNING 3 [file md_pull.mdp, line 62]:
  Unknown left-hand 'pull_rate1' in parameter file



WARNING 4 [file md_pull.mdp, line 62]:
  Unknown left-hand 'pull_k1' in parameter file



NOTE 2 [file md_pull.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.


NOTE 3 [file md_pull.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy


NOTE 4 [file md_pull.mdp]:
  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

Setting the LD random seed to 1032180820
Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_D'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_E'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...
Removing all charge groups because cutoff-scheme=Verlet
The center of mass of the position restraint coord's is  3.265  2.171  2.977
The center of mass of the position restraint coord's is  3.265  2.171  2.977

-------------------------------------------------------
Program gmx, VERSION 5.0.2
Source code file:
/home/nima/Documents/Gromacs-Program/gromacs-5.0.2/src/gromacs/gmxpreprocess/readpull.c,
line: 257

Fatal error:
Group pull_group1 required by grompp was undefined.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Best Regards,
Nima Soltani
----------------------------------------------------------
Graduate Student of Physical Chemistry
Department of Chemistry,
Sharif University of Technology.
=================================

---------- Forwarded message ----------
From: Nima Soltani <nima.slt at gmail.com>
Date: Sat, Feb 28, 2015 at 3:34 AM
Subject: Umbrella sampling Tutorial Fatal Error
To: gmx-users at gromacs.org


Hi Dear Gromacs Users
I am following umbrella sampling tutorial provided by Dr Justin Lemkul
(This tutorial is not updated for Gromacs 5 However I am using Gromacs
5.0.2 and i am trying my best to use files and commands compatible with
version 5)

I have done all the parts up to pulling section very well
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
but at the stage that I want to generate pull.tpr file it gives me a fatal
Error:
"Fatal error:
Group pull_group1 required by grompp was undefined."
I Checked spelling of "Chain_A" that i named, utilizing "mgx make_ndx"
command at previous step
Any advice or guidance would be greatly appreciated
Best Regards,
Nima Soltani
----------------------------------------------------------
Graduate Student of Physical Chemistry
Department of Chemistry,
Sharif University of Technology.
=================================