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执行水中的溶菌酶教程时生成不了tpr文件 已有1人参与
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D:\gromacs\my test> grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr :-) G R O M A C S (-: Giving Russians Opium May Alter Current Situation :-) VERSION 4.5.4 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, P?r Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. 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 ions.mdp Input grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c 1AKI_solv.gro Input Structure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt. Index file -p topol.top Input Topology file -pp processed.top Output, Opt. Topology file -o ions.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 Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -nice int 0 Set the nicelevel -[no]v bool no 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. Not for normal use and may generate unstable systems -[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 Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' NOTE 1 [file topol.top, line 18406]: System has non-zero total charge: 8.000000e+000 ------------------------------------------------------- Program grompp, VERSION 4.5.4 Source code file: ..\..\..\source\src\kernel\grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (1AKI_solv.gro, 34456) does not match topology (topol.top, 1960) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "Why Do *You* Use Constraints ?" (H.J.C. Berendsen |
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10楼2020-01-08 15:21:54
声梦奇缘001
木虫 (正式写手)
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2楼2015-09-26 15:02:23
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这是我前面执行过的语句： 1；pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce 2; editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic 3; genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top 4;grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr 我是一个超新手，以前没有任何分子模拟的经验，也没有学过相关课程。今天下午我又重新操作了一遍，执行到第四句时出现了新的错误：no molecules were defined in the systerm.我崩溃了！这个教程我已经弄了快一星期了，就是卡在第四句上。求指点! |
3楼2015-09-26 16:57:25
4楼2015-10-01 15:25:08
