[gmx-users] .tdr file not created

[Justin A. Lemkul]

sakthi kumaran wrote:
> Sorry. I will make my statements clear here after.
> here is the terminal output  after executing grompp -v
> 
>                          :-)  G  R  O  M  A  C  S  (-:
>                    Great Red Oystrich Makes All Chemists Sane
>                             :-)  VERSION 4.0.7  (-:
> 
>       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 <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.
>                                 :-)  grompp  (-:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f     grompp.mdp  Input, Opt.  grompp input file with MD parameters
>  -po      mdout.mdp  Output       grompp input file with MD parameters
>   -c       conf.gro  Input        Structure file: gro g96 pdb tpr tpb tpa
>   -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>  -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>   -n      index.ndx  Input, Opt.  Index file
>   -p      topol.top  Input        Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o      topol.tpr  Output       Run input file: tpr tpb tpa
>   -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>   -e       ener.edr  Input, Opt.  Energy file: edr ene
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -nice        int    0       Set the nicelevel
> -[no]v       bool   yes     Be loud and noisy
> -time        real   -1      Take frame at or first after this time.
> -[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
>                             sites
> -maxwarn     int    0       Number of allowed warnings during input 
> processing
> -[no]zero    bool   no      Set parameters for bonded interactions without
>                             defaults to zero instead of generating an error
> -[no]renum   bool   yes     Renumber atomtypes and minimize number of
>                             atomtypes
> Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'cpp'
> Ignoring obsolete mdp entry 'domain-decomposition'
> Replacing old mdp entry 'unconstrained-start' by 'continuation'
> Ignoring obsolete mdp entry 'dihre-tau'
> Ignoring obsolete mdp entry 'nstdihreout'
> Ignoring obsolete mdp entry 'nstcheckpoint'
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> WARNING 1 [file grompp.mdp, line unknown]:
>   Unknown or double left-hand 'bd-temp' in parameter file
> 
> checking input for internal consistency...
> NOTE 1 [file grompp.mdp, line unknown]:
>   The Berendsen thermostat does not generate the correct kinetic energy
>   distribution. You might want to consider using the V-rescale thermostat.
> processing topology...
> Opening library file /usr/share/gromacs/top/ffgmx.itp
> Opening library file /usr/share/gromacs/top/ffgmxnb.itp
> Opening library file /usr/share/gromacs/top/ffgmxbon.itp
> Opening library file /usr/share/gromacs/top/ff_dum.itp
> Opening library file /usr/share/gromacs/top/spc.itp
> Generated 1284 of the 1485 non-bonded parameter combinations
> Excluding 2 bonded neighbours molecule type 'SOL'
> processing coordinates...
> double-checking input for internal consistency...
> Velocities were taken from a Maxwell distribution at 300 K
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Analysing residue names:
> Opening library file /usr/share/gromacs/top/aminoacids.dat
> There are:   216      OTHER residues
> There are:     0    PROTEIN residues
> There are:     0        DNA residues
> Analysing Other...
> Making dummy/rest group for Acceleration containing 648 elements
> Making dummy/rest group for Freeze containing 648 elements
> Making dummy/rest group for Energy Mon. containing 648 elements
> Making dummy/rest group for VCM containing 648 elements
> Number of degrees of freedom in T-Coupling group System is 1293.00
> Making dummy/rest group for User1 containing 648 elements
> Making dummy/rest group for User2 containing 648 elements
> Making dummy/rest group for XTC containing 648 elements
> Making dummy/rest group for Or. Res. Fit containing 648 elements
> Making dummy/rest group for QMMM containing 648 elements
> T-Coupling       has 1 element(s): System
> Energy Mon.      has 1 element(s): rest
> Acceleration     has 1 element(s): rest
> Freeze           has 1 element(s): rest
> User1            has 1 element(s): rest
> User2            has 1 element(s): rest
> VCM              has 1 element(s): rest
> XTC              has 1 element(s): rest
> Or. Res. Fit     has 1 element(s): rest
> QMMM             has 1 element(s): rest
> Checking consistency between energy and charge groups...
> NOTE 2 [file grompp.mdp, line unknown]:
>   You are using a plain Coulomb cut-off, which might produce artifacts.
>   You might want to consider using PME electrostatics.
> 
> This run will generate roughly 1 Mb of data
> writing run input file...
> There were 2 notes
> There was 1 warning
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: ../../../../src/gmxlib/gmx_fatal.c, line: 481
> Fatal error:
> Too many warnings (1), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> -------------------------------------------------------
> "And You Will Know That My Name is the Lord When I Lay My Vengeance Upon 
> Thee." (Pulp Fiction)
>  

Please make note of the big, bold WARNING a few lines up.  This is the cause of 
the fatal error.  As I warned you before, some of the demo files are outdated 
and will not work.  There is far more tutorial material available from the 
Gromacs site that (I think) is more instructive than the simple examples 
provided as part of the demo.  Unfortunately, it appears that the Gromacs site 
is down, so you won't be able to access all of the tutorial material, so either 
wait for the site to come back up or fix the .mdp file so that it contains 
sensible parameters.

-Justin

> 
> *after executing gmxdump the error is *
> 
> ** 
> 
> gmxdump -s topol.tpr | more
>                          :-)  G  R  O  M  A  C  S  (-:
>                Go Rough, Oppose Many Angry Chinese Serial killers
>                             :-)  VERSION 4.0.7  (-:
> 
>       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 <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.
>                                :-)  gmxdump  (-:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -s      topol.tpr  Input, Opt!  Run input file: tpr tpb tpa
>   -f       traj.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
>   -e       ener.edr  Input, Opt.  Energy file: edr ene
>  -cp      state.cpt  Input, Opt.  Checkpoint file
>   -p      topol.top  Input, Opt.  Topology file
> -mtx    hessian.mtx  Input, Opt.  Hessian matrix
>  -om     grompp.mdp  Output, Opt. grompp input file with MD parameters
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -nice        int    0       Set the nicelevel
> -[no]nr      bool   yes     Show index numbers in output (leaving them out
>                             makes comparison easier, but creates a useless
>                             topology)
> -[no]sys     bool   no      List the atoms and bonded interactions for the
>                             whole system instead of for each molecule type
> 
> -------------------------------------------------------
> Program gmxdump, VERSION 4.0.7
> Source code file: ../../../../src/gmxlib/gmxfio.c, line: 737
> Can not open file:
> topol.tpr
> -------------------------------------------------------
> "I Need Love, Not Games" (Iggy Pop & Kate Pierson)
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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