[gmx-users] problem with gmx solvate

[David van der Spoel]

On 08/02/17 23:48, Victor Rosas Garcia wrote:
> Hello everybody,
>
> I am having problems with gmx solvate.  I am trying to solvate a small
> peptide with a solvent shell 1.2 nm thick.  When I use the following
> command line:
>
> gmx solvate -cp ../after_em.gro -cs spc216 -o b4em_sol.gro -shell 1.2 -p
> ../topol.top
>
> I get the following message:
>
>                      :-) GROMACS - gmx solvate, 2016.2 (-:
>
>                             GROMACS is written by:
>      Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par
> Bjelkmar
>  Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof
>  Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios
> Karkoulis
>     Peter Kasson        Jiri Kraus      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
>   Teemu Virolainen  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) 2001-2015, 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
> under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
>
> GROMACS:      gmx solvate, version 2016.2
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Working dir:  /home/vrosas/2017/11grupoinv/tutorialConservacion/ala10/ALPHA
> Command line:
>   gmx solvate -cp ../after_em.gro -cs spc216 -o b4em_sol.gro -shell 1.2 -p
> ../topol.top
>
> Reading solute configuration
> Protein
> Containing 112 atoms in 12 residues
> Reading solvent configuration
> 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
> Containing 648 atoms in 216 residues
>
> Initialising inter-atomic distances...
>
> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>          based on residue and atom names, since they could not be
>          definitively assigned from the information in your input
>          files. These guessed numbers might deviate from the mass
>          and radius of the atom type. Please check the output
>          files if necessary.
>
> NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
> from the source below. This means the results may be different
> compared to previous GROMACS versions.
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> A. Bondi
> van der Waals Volumes and Radii
> J. Phys. Chem. 68 (1964) pp. 441-451
> -------- -------- --- Thank You --- -------- --------
>
> Generating solvent configuration
> Will generate new solvent configuration of 4x4x4 boxes
> Solvent box contains 25131 atoms in 8377 residues
> Removed 4044 solvent atoms due to solvent-solvent overlap
> Removed 21087 solvent atoms due to solute-solvent overlap
> Sorting configuration
> Found 0 different molecule types:
> Generated solvent containing 0 atoms in 0 residues
> Writing generated configuration to b4em_sol.gro
>
> Back Off! I just backed up b4em_sol.gro to ./#b4em_sol.gro.8#
>
> Output configuration contains 112 atoms in 12 residues
> Volume                 :         216 (nm^3)
> Density                :      6.4369 (g/l)
> Number of SOL molecules:      0
>
> Processing topology
>
> Back Off! I just backed up ../topol.top to ../#topol.top.8#
>
> GROMACS reminds you: "Keep Your Shoes and Socks On, People" (F. Zappa)
>
>
> indicating zero solvent molecules were added.  Am I doing something wrong
> with the gmx solvent options?
>
> the gro and the top files I am using can be found at:
> https://www.dropbox.com/s/wjtfoj6c2sufv14/after_em.gro?dl=0
> https://www.dropbox.com/s/n02pw7bel4qwe4l/topol.top?dl=0
>
> Regards
>
> Victor
>
Apparently the -shell option does something fishy. Removing it makes the 
program work. Unless you want a spherical shell around your program you 
should not use the -shell option. Nevertheless I put in a bug report:

https://redmine.gromacs.org/issues/2119

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se