VMD-L Mailing List
From: sunyeping (sunyeping_at_aliyun.com)
Date: Tue Dec 30 2014 - 19:13:35 CST
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Dear Brain,Thank you for your reply. The script is workable now. variable b is set after "foreach water $waters {"; the result of lsort should be assigned to another variable and use the option -real: set t1 [lsort -real $t]; the first element should be the minimum of the list t1, so "set min [lindex t1 0].
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
------------------------------------------------------------------发件人:Bennion, Brian <bennion1_at_llnl.gov>发送时间:2014年12月31日(星期三) 01:47收件人:vmd-l <vmd-l_at_ks.uiuc.edu>主 题:RE: vmd-l: a script to count the frames in which some water molecules interact with selected protein atoms
P {margin-top: 0;margin-bottom: 0;}
Where do you set the variable b?
Brian
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of sunyeping [sunyeping_at_aliyun.com]
Sent: Monday, December 29, 2014 10:39 PM
To: vmd-l
Subject: vmd-l: a script to count the frames in which some water molecules interact with selected protein atoms
Dear all,
I compsed the follow script to count the frames in which some water molecules interact with selected protein atoms
set n [molinfo top get numframes]
set pockect_A [atomselect top "segname P1 and resid 7 45 59 63 66 69 159 171"]
set a [$pockect_A get index]
set wat1 [atomselect top "segname WT1 and resid 2828"]
set wat2 [atomselect top "segname WT1 and resid 8173"]
set wat3 [atomselect top "segname WT4 and resid 2284"]
set wat4 [atomselect top "segname WT4 and resid 6029"]
set wat5 [atomselect top "segname WT5 and resid 2201"]
set wat6 [atomselect top "segname WT7 and resid 8622"]
set waters [list $wat1 $wat2 $wat3 $wat4 $wat5 $wat6]
set file [open count_frame_water.dat w]
set loop_count 0
foreach water $waters {
incr loop_count
puts -nonewline $file water$loop_count
for {set i 0} {$i<$n} {incr i} {
foreach ai $a {
foreach bj $b {
lappend t [measure bond "$ai $bj" frame $i]
}
}
lsort -decreasing $t; set max [lindex $t 0]
if { $max<=3.5} {
puts -nonewline $file $i
}
puts $file \n
}
}
close $file
It cannot work properly. It seems that the foreach loop of
foreach water $waters is carried inly once. Could you check it and find what are the faults of it?
Thanks
in advance.
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
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