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. V16.16
___ ___ ___ ___
 | / | / | / | 
_|_/\_|_/\_|_/\_|_

| Date/time: 03/01/19 11:14:02
| 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:
 0: 'trpzip2.ff10.mbondi.parm7', 220 atoms, 13 res, box: None, 1 mol

> parminfo 0
Topology trpzip2.ff10.mbondi.parm7 contains 220 atoms.
    13 residues.
    1 molecules.
    227 bonds (104 to H, 123 other).
    402 angles (233 with H, 169 other).
    853 dihedrals (481 with H, 372 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:
 0: 'trpzip2.gb.nc' is a NetCDF AMBER trajectory, Parm trpzip2.ff10.mbondi.parm7 (reading 1201 of 1201)
  Coordinate processing will occur on 1201 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
    1 SER      1    13    13     1
    2 TRP     14    37    24     2
    3 THR     38    51    14     3
    4 TRP     52    75    24     4
    5 GLU     76    90    15     5
    6 ASN     91   104    14     6
    7 GLY    105   111     7     7
    8 LYS    112   133    22     8
    9 TRP    134   157    24     9
   10 THR    158   171    14    10
   11 TRP    172   195    24    11
   12 LYS    196   217    22    12
   13 NHE    218   220     3    13

> atominfo :13
#Atom Name  #Res Name  #Mol Type   Charge     Mass GBradius El
  218 N       13 NHE      1 N     -0.4630  14.0100   1.5500  N
  219 HN1     13 NHE      1 H      0.2315   1.0080   1.3000  H
  220 HN2     13 NHE      1 H      0.2315   1.0080   1.3000  H

> distance end-to-end :1 :13 out dist-end-to-end.agr
   DISTANCE: :1 to :13, center of mass.

> list actions
ACTIONS:
  0: [distance end-to-end :1 :13 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:
 0: 'trpzip2.ff10.mbondi.parm7', 220 atoms, 13 res, box: None, 1 mol, 1201 frames

INPUT TRAJECTORIES:
 0: 'trpzip2.gb.nc' is a NetCDF AMBER trajectory, Parm trpzip2.ff10.mbondi.parm7 (reading 1201 of 1201)
  Coordinate processing will occur on 1201 frames.
TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'trpzip2.ff10.mbondi.parm7' (1 actions):
  0: [distance end-to-end :1 :13 out dist-end-to-end.agr]
    :1 (13 atoms) to :13 (3 atoms), imaging off.
----- trpzip2.gb.nc (1-1201, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 1201 frames and processed 1201 frames.
TIME: Trajectory processing: 0.0094 s
TIME: Avg. throughput= 127372.9982 frames / second.

ACTION OUTPUT:
DATASETS:
  1 data set:
    end-to-end "end-to-end" (double, distance), size is 1201

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
       1       6.4251
       2       5.9250
       3       6.7926
       4       6.3125
       5       5.7580
       6       5.4389
       7       6.1086
       8       6.5588
       9       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., 2013, 9 (7), pp 3084-3095.

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 :1 :13 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