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ptf1242

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[交流] 【求助】manual 运行不了已有4人参与

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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