VMD-L Mailing List

From: 本村肇 (h-motomura_at_bioreg.kyushu-u.ac.jp)
Date: Tue Dec 19 2017 - 22:01:20 CST

Thank you for your help.
The following script worked well.

set seltext1 "name CG and resid 26"
set sel1 [atomselect top "$seltext1"]
set seltext2 "name CG and resid 30"
set sel2 [atomselect top "$seltext2"]
measure bond [lindex [$sel1 get index] 0] [lindex [$sel2 get index] 0]

Next, I would like to output the distances of all frames to txt file (or dat file).
However, I do not know how to use the data frame in VMD command.
How should I export them to txt file?
I have an following idea.
Could you tell me the completed script?

mol load psf ***.psf dcd ***.dcd
set nf [molinfo top get numframes]
(make a data frame)
for {set i 0} {$i < $nf} {incr i} {
(select frame i)
set seltext1 "name CG and resid 26"
set sel1 [atomselect top "$seltext1"]
set seltext2 "name CG and resid 30"
set sel2 [atomselect top "$seltext2"]
measure bond [lindex [$sel1 get index] 0] [lindex [$sel2 get index] 0]
(input to a data frame)
}
(export a data frame as a txt file)
______________________________
九州大学大学院 システム生命科学府
システム生命科学専攻2年
学籍番号3SL16068S
生体防御医学研究所
神田研究室 本村肇
E-mail：h-motomura_at_bioreg.kyushu-u.ac.jp
E-mail（携帯）：hajime.motomura.bioreg.kyushu_at_gmail.com
TEL（携帯）：090-7443-4138

> 2017/12/20 3:09、Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>のメール:
>
> If you want the distance between selections, the easiest thing to do is to measure the distance between the center of the selections:
>
> veclength [vecsub [measure center $sel1] [measure center $sel2]]
>
> Measure bond works on atomic indices. So if you wanted to get the distance between the first atoms in two selections, you could do something like this:
>
> measure bond [lindex [$sel1 get index] 0] [lindex [$sel2 get index] 0]
>
> -Josh
>
> On 12/19/2017 06:12 AM, Ashar Malik wrote:
> Now $sel1 and $sel2 are the selections. But the documentation of the measure bond says:
>
> The atoms are specified in form of a list of atom indexes
>
> Not selections of atom themselves. So you need to get the index of the atoms.
>
> You can do this:
>
> set seltext1 "name CG and resid 26"
> set sel1 [[atomselect top "$seltext1"] get index]
> set seltext2 "name CG and resid 30"
> set sel2 [[atomselect top "$seltext2"] get index]
> measure bond [list $sel1 $sel2]
>
> I am not sure since I haven't tried this - but it shoudl theoretically work.
>
> On Tue, Dec 19, 2017 at 10:03 PM, 本村肇 <h-motomura_at_bioreg.kyushu-u.ac.jp<mailto:h-motomura_at_bioreg.kyushu-u.ac.jp>> wrote:
> I am sorry, I corrected my script.
>
> vmd > set seltext1 "name CG and resid 26"
> vmd > set sel1 [atomselect top "$seltext1"]
> vmd > set seltext2 "name CG and resid 30"
> vmd > set sel2 [atomselect top "$seltext2"]
> vmd > measure bond {$sel1 $sel2}
> expected integer but got "$sel1" measure bond: bad atom index
>
>> 2017/12/19 17:42、Ashar Malik <asharjm_at_gmail.com<mailto:asharjm_at_gmail.com>>のメール:
>>
>> I didn't have a detailed look at this but
>>
>> vmd > set seltext1 "name CG and resid 26”
>> vmd > set seltext2 "name CG and resid 30”
>> vmd > measure bond {$sel1 $sel2}
>>
>> what is $sel1 and $sel2???
>>
>> your selections are called seltext1 and seltext2 not sel1 and sel2.
>>
>> On Tue, Dec 19, 2017 at 8:56 PM, 本村肇 <h-motomura_at_bioreg.kyushu-u.ac.jp<mailto:h-motomura_at_bioreg.kyushu-u.ac.jp>> wrote:
>> Dear all,
>>
>> I would like to measure bond length with “name ** and resid **” in scripts.
>>
>> vmd > set seltext1 "name CG and resid 26”
>> vmd > set seltext2 "name CG and resid 30”
>> vmd > measure bond {$sel1 $sel2}
>> expected integer but got "$sel1" measure bond: bad atom index
>>
>> However the following command succeed.
>> vmd > measure bond {113 140}
>> 11.772942543029785
>>
>> I configured that the above atoms existed.
>> How can I measure bond length with “name ** and resid **" in scripts?
>>
>> Sincerely,
>> Hajime Motomura
>>
>>
>>
>>
>> --
>> Best,
>> /A
>
>
>
>
>
> --
> Best,
> /A