From: jiali wang (jialiwangnamd_at_gmail.com)
Date: Sat Feb 13 2021 - 22:33:16 CST
Dear Peter,
Thank you so much for your suggestions. let me work on this and get back to
you.
best,
Jiali
On Sat, Feb 13, 2021 at 11:30 PM Peter Freddolino <petefred_at_umich.edu>
wrote:
> Ah my fault, I should have read more carefully, I assumed incorrectly that
> the variables named "$sel1", etc in the measure dihed call were atom
> selections.
> Ok, so a couple of suggestions.
> -Every time you make an atom selection, you need to explicitly delete it.
> The use of anonymous atom selections, as in your 'set sel1 ...' lines of
> code, will leave them hanging around and cause a memory leak.
>
> -Rather than do
> set selA [atomselect top "segname PP5 and name C"]
> ...
> set sel1 [[atomselect top "$selA"] get index]
> why not just do
> set selA [atomselect top "segname PP5 and name C"]
> set ind1 [$selA get index]
> (and then you'd want to add
> $selA delete
> to avoid the memory leak noted above)
>
> -at the end of the day, in tcl, using curly braces ({}) to construct a
> list does NOT allow substitution of variables. You'll instead want
> [list $ind1 $ind2 $ind3 $ind4]
> or some such
>
> Best,
> Peter
>
>
>
> On Sat, Feb 13, 2021 at 11:06 PM Jiali Wang <jwang204_at_binghamton.edu>
> wrote:
>
>> Dear Peter,
>> Thank you for your reply. I use "set sel1 [[atomselect top "$selA"] get
>> index]" to get index, is there something wrong here?
>> I am very new to the script part of calculations. I appreciate your help
>> very much.
>> best,
>> Jiali
>>
>> On Sat, Feb 13, 2021 at 7:48 PM Peter Freddolino <petefred_at_umich.edu>
>> wrote:
>>
>>> The arguments to `measure dihed` are supposed to be atom indices, not
>>> atom selections. See
>>> https://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/node124.html
>>>
>>> Best,
>>> Peter
>>>
>>> On Sat, Feb 13, 2021 at 1:56 AM jiali wang <jialiwangnamd_at_gmail.com>
>>> wrote:
>>>
>>>> Dear NAMD users,
>>>> I have an error when I calculate the dihedral angle, the calculation
>>>> performed in the VMD. code as below, but it says "expected integer but got
>>>> "$sel1" measure dihed: bad atom index". Do you know what happened?
>>>> Thank you so much!!
>>>> Jiali
>>>>
>>>> set selA [atomselect top "segname PP5 and name C"]
>>>> set selB [atomselect top "segname PP5 and name CA"]
>>>> set selC [atomselect top "segname PP5 and name CB"]
>>>> set selD [atomselect top "segname PP5 and name CG"]
>>>>
>>>> set sel1 [[atomselect top "$selA"] get index]
>>>> set sel2 [[atomselect top "$selB"] get index]
>>>> set sel3 [[atomselect top "$selC"] get index]
>>>> set sel4 [[atomselect top "$selD"] get index]
>>>>
>>>> set nf [molinfo top get numframes]
>>>> set outfile [open dihed-cal.dat w]
>>>> for {set i 0} {$i < $nf} {incr i} {
>>>>
>>>> puts "frame $i of $nf"
>>>>
>>>> set dihedlist [measure dihed {$sel1 $sel2 $sel3 $sel4}]
>>>> puts $outfile "$i $dihedlist"
>>>>
>>>
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