Question

我正在使用AMBER模拟分子系统。在AMBER中，有一个模块来分析名为＆＃34; cpptraj＆＃34;的数据。

通常我在bash脚本中使用命令如下：

#!/bin/bash


path="../Production-from-gpu"
system="maltoLyo-23per" 
top="maltoLyo23per.top" 
alltraj="md-product.center.reimage-all.traj" 
outtraj="maltoLyo-23per-reimage" 


cpptraj $top << EOF


trajin  ../$system-MD001-run0100.traj 1 100 5 
trajin  ../$system-MD001-run0200.traj 1 100 5 
trajin  ../$system-MD001-run0300.traj 1 100 5 
trajin  ../$system-MD001-run0400.traj 1 100 5 
trajin  ../$system-MD001-run0500.traj 1 100 5 
trajin  ../$system-MD001-run0600.traj 1 100 5 
trajin  ../$system-MD001-run0700.traj 1 100 5 
trajin  ../$system-MD001-run0800.traj 1 100 5 
trajin  ../$system-MD001-run0900.traj 1 100 5 
trajin  ../$system-MD001-run1000.traj 1 100 5 

trajout abc.traj mdcrd

EOF

我发现运行此脚本没有问题。

现在我想使用＆＃34;用于＆＃34;在这个脚本中循环，比如，

#!/bin/bash


path="../Production-from-gpu"
system="maltoLyo-23per" 
top="maltoLyo23per.top" 
alltraj="md-product.center.reimage-all.nc" 
outtraj="maltoLyo-23per-reimage" 



cpptraj $top << EOF

for i in {0..5};do

if [[ ($i -ge 0) && ($i -lt  10) ]]; then


trajin  $path/$system-MD00i-run0100.traj 1 100 5 
trajin  $path/$system-MD00i-run0200.traj 1 100 5 
trajin  $path/$system-MD00i-run0300.traj 1 100 5 
trajin  $path/$system-MD00i-run0400.traj 1 100 5 
trajin  $path/$system-MD00i-run0500.traj 1 100 5 
trajin  $path/$system-MD00i-run0600.traj 1 100 5 
trajin  $path/$system-MD00i-run0700.traj 1 100 5 
trajin  $path/$system-MD00i-run0800.traj 1 100 5 
trajin  $path/$system-MD00i-run0900.traj 1 100 5 
trajin  $path/$system-MD00i-run1000.traj 1 100 5 
fi


trajout abc.traj mdcrd
##############################################


done
EOF

我发现这段代码无法执行。我收到如下错误消息：

vijay@glycosim:/media/glycoExtra/TRAJECTORY-lyotropic-system300ns/maltoLyo-C12-23per/Select-traj-using-cpptraj$ ./generate_traj_select_script.sh

CPPTRAJ: Trajectory Analysis. V13.15
    ___  ___  ___  ___
     | \/ | \/ | \/ | 
    _|_/\_|_/\_|_/\_|_
    AmberParm Title: [default_name]
    Radius Set: modified Bondi radii (mbondi)
INPUT: Reading Input from STDIN
  [for i in {0..5};do]
[for]: Command not found.

vijay@glycosim:/media/glycoExtra/TRAJECTORY-lyotropic-system300ns/maltoLyo-C12-23per/Select-traj-using-cpptraj$

如何让这个脚本无问题地运行？提前感谢任何帮助。谢谢。

Answer 1

for不会在heredoc中作为循环工作。

你需要把循环放在它之外。当您将其放在heredoc内时，

for i in {0..5};do

按原样传递给程序。

此外，由于您从0循环到5，因此条件

if [[ ($i -ge 0) && ($i -lt  10) ]]; then

完全没用。您可以将代码编写为：

for i in {0..5};do

cpptraj $top << EOF

trajin  $path/$system-MD00i-run0100.traj 1 100 5 
trajin  $path/$system-MD00i-run0200.traj 1 100 5 
trajin  $path/$system-MD00i-run0300.traj 1 100 5 
trajin  $path/$system-MD00i-run0400.traj 1 100 5 
trajin  $path/$system-MD00i-run0500.traj 1 100 5 
trajin  $path/$system-MD00i-run0600.traj 1 100 5 
trajin  $path/$system-MD00i-run0700.traj 1 100 5 
trajin  $path/$system-MD00i-run0800.traj 1 100 5 
trajin  $path/$system-MD00i-run0900.traj 1 100 5 
trajin  $path/$system-MD00i-run1000.traj 1 100 5 

trajout abc.traj mdcrd

EOF

done

Answer 2

尝试在if和for循环中移动cpptraj命令。 cpptraj可能不是unix shell提示符。

在bash脚本中使用EOF

2 个答案: