24小时热门版块排行榜

返回列表

白玉浴血

木虫 (正式写手)

应助: 0 (幼儿园)
金币: 2513.6
帖子: 838
在线: 243.2小时
虫号: 2684358

[交流] 请问这是什么情况？

pdb2gmx_mpid -f SNS.pdb -o sns.gro -p sns.top -i sns.itp输入进去它之后
:-)  G  R  O  M  A  C  S  (-:

                        GROtesk MACabre and Sinister

                        :-)  VERSION 4.6.3  (-:

      Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
         Herman J.C. Berendsen, Aldert van Buuren, P盲r Bjelkmar,
   Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
      Peter Kasson, Carsten Kutzner, 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) 2001-2012,2013, 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 Lesser General Public License
      as published by the Free Software Foundation; either version 2.1
         of the License, or (at your option) any later version.

               :-)  pdb2gmx_mpid (double precision)  (-:

Option    Filename  Type       Description
------------------------------------------------------------
  -f       SNS.pdb  Input       Structure file: gro g96 pdb tpr etc.
  -o       sns.gro  Output    Structure file: gro g96 pdb etc.
  -p       sns.top  Output    Topology file
  -i       sns.itp  Output    Include file for topology
  -n    clean.ndx  Output, Opt. Index file
  -q    clean.pdb  Output, Opt. Structure file: gro g96 pdb etc.

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
-chainsep enum id_or_ter  Condition in PDB files when a new chain should
                        be started (adding termini): id_or_ter,
                        id_and_ter, ter, id or interactive
-merge    enum no    Merge multiple chains into a single
                        [moleculetype]: no, all or interactive
-ff       string select  Force field, interactive by default. Use -h for
                        information.
-water    enum select  Water model to use: select, none, spc, spce,
                        tip3p, tip4p or tip5p
-[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, instead of charged
                        (default)
-[no]lys    bool no    Interactive lysine selection, instead of charged
-[no]arg    bool no    Interactive arginine selection, instead of charged
-[no]asp    bool no    Interactive aspartic acid selection, instead of
                        charged
-[no]glu    bool no    Interactive glutamic acid selection, instead of
                        charged
-[no]gln    bool no    Interactive glutamine selection, instead of
                        neutral
-[no]his    bool no    Interactive histidine selection, instead of
                        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 coordinate
                        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
-[no]chargegrp bool yes    Use charge groups in the .rtp file
-[no]cmap bool yes    Use cmap torsions (if enabled in the .rtp file)
-[no]renum bool no    Renumber the residues consecutively in the output
-[no]rtpres  bool no    Use .rtp entry names as residue names

Select the Force Field:
From '/home/gromacs/programs/gromacs4.6/share/gromacs/top':
1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
8: CHARMM27 all-atom force field (with CMAP) - version 2.0
9: cnt_oplsaa
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
17: [DEPRECATED] Encad all-atom force field, using full solvent charges
18: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
19: [DEPRECATED] Gromacs force field (see manual)
20: [DEPRECATED] Gromacs force field with hydrogens for NMR
也不出现拓扑文件，这是什么情况？改怎样生成拓扑文件呢？

回复此楼