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【求助】manual 运行不了 已有4人参与
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就是安装手册方法来，但是压根生成不了 top 和 gro 文件。结果是： File input/output error ... 请问是哪里有问题？ 我用的是最新的gromacs版本，ubuntu 系统。也装了个gfortran等。生成不了top 和 gro 文件，就没法进行生成后面的tpr。 我晓得前面的水 ，甲醇 ，mixed那几个教程是没法运行的。但是听说 speptide 可以运行。但是就是有这个小问题。 已经进入了speptide 目录下面。 用的命令也是对的。但是就是生成不了top 和 gro 文件。 ptf1242@ptf1242-laptop:/usr/share/gromacs/tutor/speptide$ pdb2gmx -f speptide.pdb -p speptide.top -o speptide.gro :-) G R O M A C S (-: Gravel Rubs Often Many Awfully Cauterized Sores :-) 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 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. :-) pdb2gmx (-: Option Filename Type Description ------------------------------------------------------------ -f speptide.pdb Input Structure file: gro g96 pdb tpr tpb tpa -o speptide.gro Output Structure file: gro g96 pdb -p speptide.top Output Topology file -i posre.itp Output Include file for topology -n clean.ndx Output, Opt. Index file -q clean.pdb Output, Opt. Structure file: gro g96 pdb Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -[no]merge bool no Merge chains into one molecule definition -ff string select Force field, interactive by default. Use -h for information. -water enum spc Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p or f3c -[no]inter bool no Set the next 8 options to interactive -[no]ss bool no Interactive SS bridge selection -[no]ter bool no Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]arg bool no Interactive Arganine selection, iso charged -[no]asp bool no Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged -[no]gln bool no Interactive Glutamine selection, iso neutral -[no]his bool no Interactive Histidine selection, iso checking H-bonds -angle real 135 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) -dist real 0.3 Maximum donor-acceptor distance for a H-bond (nm) -[no]una bool no Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine -[no]ignh bool no Ignore hydrogen atoms that are in the pdb file -[no]missing bool no Continue when atoms are missing, dangerous -[no]v bool no Be slightly more verbose in messages -posrefc real 1000 Force constant for position restraints -vsite enum none Convert atoms to virtual sites: none, hydrogens or aromatics -[no]heavyh bool no Make hydrogen atoms heavy -[no]deuterate bool no Change the mass of hydrogens to 2 amu Opening library file /usr/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6: [DEPRECATED] Gromacs force field (see manual) 7: [DEPRECATED] Gromacs force field with hydrogens for NMR 8: Encad all-atom force field, using scaled-down vacuum charges 9: Encad all-atom force field, using full solvent charges 0 Opening library file /usr/share/gromacs/top/ffG43a1.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Opening library file /usr/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /usr/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /usr/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /usr/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /usr/share/gromacs/top/elements.dat Entries in elements.dat: 218 Reading speptide.pdb... Read 146 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 19 residues with 146 atoms chain #res #atoms 1 ' ' 19 146 All occupancies are one Opening library file /usr/share/gromacs/top/ffG43a1.atp Atomtype 1 Reading residue database... (ffG43a1) Opening library file /usr/share/gromacs/top/ffG43a1.rtp Residue 96 Sorting it all out... Opening library file /usr/share/gromacs/top/ffG43a1.hdb Opening library file /usr/share/gromacs/top/ffG43a1-n.tdb Opening library file /usr/share/gromacs/top/ffG43a1-c.tdb ------------------------------------------------------- Program pdb2gmx, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/futil.c, line: 300 File input/output error: speptide.top ------------------------------------------------------- "You Look Better Upside Down" (Throwing Muses) ptf1242@ptf1242-laptop:/usr/share/gromacs/tutor/speptide$ |
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