VMD-L Mailing List

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Tue Feb 18 2014 - 13:26:22 CST

Hi Roy,

Try “protein or resname LIG or same residue as (water within 10 of resname LIG)”

Maxim

On Feb 18, 2014, at 1:17 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> You send your message to the wrong address. Send your VMD-L
> messages to:
> vmd-l_at_ks.uiuc.edu
>
> Mail to other addresses will bounce or be silently dropped.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Feb 18, 2014 at 09:31:06AM -0600, KK R wrote:
>> Hi,
>> I have a result from NAMD simulation. I noticed that there were two water
>> clusters around the ligand within the active site of the protein.
>> Therefore, I tried to extract a set of protein+ligand+water (within 10A of
>> ligand) from every frame of my DCD trajectory. I could accomplish it using
>> the following script in the Tk console.
>> --------------------------------------------------------------------------------------------------------------------------------
>> set sel [atomselect top "{protein} or {resname LIG} or {water within 10 of
>> (resname LIG)}"]
>> set n [molinfo top get numframes]
>> set outname "protligwater_"
>> for { set i 0 } { $i < $n } { incr i } {
>> $sel frame $i
>> $sel update
>> set name [format "%s%.9d.pdb" $outname $i]
>> $sel writepdb $name
>> }
>> ---------------------------------------------------------------------------------------------------------------------------------
>> where LIG is the segid for ligand
>>
>> But, the above script writes protein+ligand+(water residues as well as
>> only part of water residues (like H or OH etc) lying within that radius
>> around ligand).
>> How to specify in the command line to select complete water residues lying
>> within any particular radius, even if only part of some water resides with
>> that radius?
>>
>> I hope that my question is clear to you all. If not, please let me know.
>> Thanks again,
>> Best regards,
>> Roy
>
> --
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> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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