标题: VMD模拟 writepdb命令无法生成并修改新的pdb文件 [打印本页] 作者Author: 伶俜徒奈何 时间: 2024-3-29 15:20 标题: VMD模拟 writepdb命令无法生成并修改新的pdb文件 如题
VMD为32位x86的1.9.3版本，系统是WIN10 64位，安装目录为C:\md\VMD
运行文献提供的的tcl脚本，目的是将反应的单体分子随即分配到pbc盒中
在 $all writepdb pdb/${chain_name}_${id}_temp.pdb处报错为：Unable to open file pdb/A_489_temp.pdb for writing ERROR) Unable to open file pdb/A_489_temp.pdb of type pdb for writing frames.
下为该tcl完整代码：（其中mol_name,xyzpbc,chain_list均在上一步tcl全局变量中定义并赋值）
proc rand_position {chain_name id} {
global mol_name
global xpbc
global ypbc
global zpbc
# set segname and chain name
set all [atomselect top all]
$all set chain ${chain_name}
$all set segname ${chain_name}${id}
# rotate the added molecules in different direction
set rot_x [expr rand()*360]
set rot_y [expr rand()*360]
set rot_z [expr rand()*360]
# randomly rotate molecule in different direction
$all move [trans center {0 0 0} x $rot_x]
$all move [trans center {0 0 0} y $rot_y]
$all move [trans center {0 0 0} z $rot_z]
# randomly distribute monomer in the pbc box
set movex [expr rand()*($xpbc-10)]
set movey [expr rand()*($ypbc-10)]
set movez [expr rand()*($zpbc-10)]
$all moveby "$movex $movey $movez"
# creat pdb files for each monomer
$all writepdb pdb/${chain_name}_${id}_temp.pdb