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gromacs最终合并输出pdb文件

作者:小宝 2017-03-26 14:03:44

为了方便使用可视化软件查看模拟的结果,经常需要将结果合并成pdb等文件,然后用shell远程下载文件后查看。

用trjconv 命令合并生产文件,-s 输入tpr能量文件,-f 输入xtc文件,最后-o表示输出文件。-pbc 后面的

是表示读取里面的数据,后面需要选择,命令如下:

trjconv -s dppc-md.tpr -f dppc-md.xtc -o dppc-md.pdb -pbc whole -conect


 :-)  trjconv  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -f    dynamic.xtc  Input        Trajectory: xtc trr trj gro g96 pdb cpt
  -o    dynamic.pdb  Output       Trajectory: xtc trr trj gro g96 pdb
  -s    dynamic.tpr  Input, Opt!  Structure+mass(db): tpr tpb tpa gro g96 pdb
  -n      index.ndx  Input, Opt.  Index file
 -fr     frames.ndx  Input, Opt.  Index file
-sub    cluster.ndx  Input, Opt.  Index file
-drop      drop.xvg  Input, Opt.  xvgr/xmgr 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    19      Set the nicelevel
-b           time   0       First frame (ps) to read from trajectory
-e           time   0       Last frame (ps) to read from trajectory
-tu          enum   ps      Time unit: fs, ps, ns, us, ms or s
-[no]w       bool   no      View output .xvg, .xpm, .eps and .pdb files
-xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-skip        int    1       Only write every nr-th frame
-dt          time   0       Only write frame when t MOD dt = first time (ps)
-[no]round   bool   no      Round measurements to nearest picosecond
-dump        time   -1      Dump frame nearest specified time (ps)
-t0          time   0       Starting time (ps) (default: don't change)
-timestep    time   0       Change time step between input frames (ps)
-pbc         enum   whole   PBC treatment (see help text for full
                            description): none, mol, res, atom, nojump,
                            cluster or whole
-ur          enum   rect    Unit-cell representation: rect, tric or compact
-[no]center  bool   no      Center atoms in box
-boxcenter   enum   tric    Center for -pbc and -center: tric, rect or zero
-box         vector 0 0 0   Size for new cubic box (default: read from input)
-clustercenter vector 0 0 0   Optional starting point for pbc cluster option
-trans       vector 0 0 0   All coordinates will be translated by trans. This
                            can advantageously be combined with -pbc mol -ur
                            compact.
-shift       vector 0 0 0   All coordinates will be shifted by framenr*shift
-fit         enum   none    Fit molecule to ref structure in the structure
                            file: none, rot+trans, rotxy+transxy,
                            translation, transxy or progressive
-ndec        int    3       Precision for .xtc and .gro writing in number of
                            decimal places
-[no]vel     bool   yes     Read and write velocities if possible
-[no]force   bool   no      Read and write forces if possible
-trunc       time   -1      Truncate input trajectory file after this time
                            (ps)
-exec        string         Execute command for every output frame with the
                            frame number as argument
-[no]app     bool   no      Append output
-split       time   0       Start writing new file when t MOD split = first
                            time (ps)
-[no]sep     bool   no      Write each frame to a separate .gro, .g96 or .pdb
                            file
-nzero       int    0       If the -sep flag is set, use these many digits
                            for the file numbers and prepend zeros as needed
-dropunder   real   0       Drop all frames below this value
-dropover    real   0       Drop all frames above this value
-[no]conect  bool   yes     Add conect records when writing .pdb files.
                            Useful for visualization of non-standard
                            molecules, e.g. coarse grained ones


And the next is to choose which part you want to fill :

Reading file dynamic.tpr, VERSION 4.6.5 (single precision)
Select group for output
Group     0 (         System) has   906 elements
Group     1 (        Protein) has   163 elements
Group     2 (      Protein-H) has   163 elements
Group     3 (        C-alpha) has     0 elements
Group     4 (       Backbone) has     0 elements
Group     5 (      MainChain) has     0 elements
Group     6 (   MainChain+Cb) has     0 elements
Group     7 (    MainChain+H) has     0 elements
Group     8 (      SideChain) has   163 elements
Group     9 (    SideChain-H) has   163 elements
Group    10 (    Prot-Masses) has   163 elements
Group    11 (    non-Protein) has   743 elements
Group    12 (          Other) has   743 elements
Group    13 (              W) has   743 elements
Select a group:

Choose "System" mean everything of this design.

可以根据自己的需要进行选择生成。0代表系统里面的全部都转换。



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