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【求助】Can not open file: topol.tpr
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http://manual.gromacs.org/current/online/water.html When I tried to follow the instructions from above links... it showed me Can not open file: topol.tpr and I cannot locate that file...seems do not exist... anybody has any ideas? Thanks! [ Last edited by zeoliters on 2009-11-13 at 18:34 ] |
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I felt quite being disappointed... Why there was only one person giving me simply answering by saying 'can say nothing about it' to let me feel some subtle guilty. Never mind, I found the answer by myself... I need to add 'sudo' when I run some comman before it came out wrong... Jotted down here, hope be helpful to the other new beginner... |
9楼2009-10-07 16:17:28
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lovely-laptop:/usr/share/gromacs/tutor/water$ ngmx :-) G R O M A C S (-: Giving Russians Opium May Alter Current Situation :-) VERSION 4.0.3 (-: 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. :-) ngmx (-: Option Filename Type Description ------------------------------------------------------------ -f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input Run input file: tpr tpb tpa -n index.ndx Input, Opt. Index file Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) ------------------------------------------------------- Program ngmx, VERSION 4.0.3 Source code file: ../../../../src/gmxlib/gmxfio.c, line: 736 Can not open file: topol.tpr ------------------------------------------------------- |
2楼2009-10-05 02:06:01
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when I run grompp it shows like that lovely-laptop:/usr/share/gromacs/tutor/water$ grompp :-) G R O M A C S (-: GROningen MAchine for Chemical Simulation :-) VERSION 4.0.3 (-: 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. :-) 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' ------------------------------------------------------- Program grompp, VERSION 4.0.3 Source code file: ../../../../src/gmxlib/futil.c, line: 298 File input/output error: mdout.mdp ------------------------------------------------------- |
3楼2009-10-05 02:14:17
4楼2009-10-05 02:41:11
