AMBER: CPPTRAJ Tutorial C0

CPPTRAJ作为PTRAJ的继任者，拥有比PTRAJ更强大的功能，本教程会简要的介绍CPPTRAJ的用法及注意事项。

需要的文件：

trpzip2.gb.nc

trpzip2.ff10.mbondi.parm7

Loading a Topology and Trajectory

使用cpptraj命令可以打开cpptraj，log文件可以在cpptraj.log中找到。

$ cpptraj　

CPPTRAJ: Trajectory Analysis. V16.
___ ___ ___ ___
 | \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_

| Date/time: // ::
| Available memory: 393.146 MB

>
# 载入拓扑文件（topology file）
> parm trpzip2.ff10.mbondi.parm7
# 可以使用list parm命令查看刚刚载入的拓扑文件，详细信息使用parminfo命令查看
> list parm
PARAMETER FILES:
 : 'trpzip2.ff10.mbondi.parm7',  atoms,  res, box: None,  mol
> parminfo
Topology trpzip2.ff10.mbondi.parm7 contains  atoms.
     residues.
     molecules.
     bonds ( to H,  other).
     angles ( with H,  other).
     dihedrals ( with H,  other).
    Box: None
    GB radii set: modified Bondi radii (mbondi)
# 载入NetCDF格式的轨迹文件（trajetory file）
>trajin trpzip2.gb.nc
Reading 'trpzip2.gb.nc' as Amber NetCDF
# 同样，可以使用list trajin命令查看刚刚载入的轨迹文件
> list trajin
INPUT TRAJECTORIES:
 : 'trpzip2.gb.nc' is a NetCDF AMBER trajectory, Parm trpzip2.ff10.mbondi.parm7 (reading  of )
  Coordinate processing will occur on  frames.

Specifying an Action

# 打印帮助信息
> help distance
　　[<name>] <mask1> <mask2> [out <filename>] [geom] [noimage] [type noe]
　　Options for 'type noe':
　　[bound <lower> bound <upper>] [rexp <expected>] [noe_strong] [noe_medium] [noe_weak]
　　Calculate distance between atoms in <mask1> and <mask2>

> resinfo
#Res  Name First  Last Natom #Orig
     SER
     TRP
     THR
     TRP
     GLU
     ASN
     GLY
     LYS
     TRP
    THR
    TRP
    LYS
    NHE                13
> atominfo :
#Atom Name  #Res Name  #Mol Type   Charge     Mass GBradius El
   N        NHE       N     -0.4630  14.0100   1.5500  N
   HN1      NHE       H      0.2315   1.0080   1.3000  H
   HN2      NHE       H      0.2315   1.0080   1.3000  H
> distance end-to-end : : out dist-end-to-end.agr
   DISTANCE: : to :, center of mass.
> list actions
ACTIONS:
  : [distance end-to-end : : out dist-end-to-end.agr]

Processing the Trajectory

# 前面的action操作是不会执行的，需要使用run命令或者go命令来执行，执行内容包括导入拓扑文件及轨迹文件，根据action (distance)处理轨迹文件，产生DATASETS及结果文件DATAFILES（dist-end-to-end.agr）等。

> run
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES:
 : 'trpzip2.ff10.mbondi.parm7',  atoms,  res, box: None,  mol,  frames

INPUT TRAJECTORIES:
 : 'trpzip2.gb.nc' is a NetCDF AMBER trajectory, Parm trpzip2.ff10.mbondi.parm7 (reading  of )
  Coordinate processing will occur on  frames.
TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'trpzip2.ff10.mbondi.parm7' ( actions):
  : [distance end-to-end : : out dist-end-to-end.agr]
    : ( atoms) to : ( atoms), imaging off.
----- trpzip2.gb.nc (-, ) -----
 % % % % % % % % % % % Complete.
Read  frames and processed  frames.
TIME: Trajectory processing: 0.0094 s
TIME: Avg. throughput= 127372.9982 frames / second.

ACTION OUTPUT:
DATASETS:
   data set:
    end-to-end "end-to-end" (double, distance), size is 

DATAFILES:
  dist-end-to-end.agr (Grace File):  end-to-end
---------- RUN END ---------------------------------------------------

# 可以直接在CPPTRAJ里执行xmgrace查看结果
> xmgrace dist-end-to-end.agr
...

Working With Data Sets

# 我们可以对前面产生的DATASET进行处理，如前面产生的”end-to-end“，我们可以使用writedata命令把数据写成标准列格式。

> writedata end-to-end.dat end-to-end
　　end-to-end

# 同样，我们可以直接在CPPTRAJ中使用linux的head命令，对数据进行查看。
> head end-to-end.dat
#Frame     end-to-end
              6.4251
              5.9250
              6.7926
              6.3125
              5.7580
              5.4389
              6.1086
              6.5588
              5.6949

# 最后我们可以使用quit命令退出CPPTRAJ。
>quit
TIME: Total execution time: 131.2112 seconds.
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
  Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
  Theory Comput., ,  (), pp -.

Running in Batch Mode

# 与tleap一样，我们也可以使用batch模式，直接提交cpptraj的参数文件。

# cpptraj.in

parm trpzip2.ff10.mbondi.parm7
trajin trpzip2.gb.nc
distance end-to-end : : out dist-end-to-end.agr
run
writedata end-to-end.dat end-to-end

运行CPPTRAJ：

$ cpptraj -i cpptraj.in

原文链接：

http://ambermd.org/tutorials/analysis/tutorial0/index.htm