VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Feb 17 2007 - 19:57:17 CST

I am not sure why specifically it doesn't work for pdb files (perhaps
the output it does give would be helpful). However, the problem with
the number of h-bonds is that the measure hbonds outputs a list of
lists (which you do make use of later in your script), not a number.

> puts ${outfile} "number of h-bonds in frame $i: $nhb"

Instead of $nhb here, put

[llength [lindex $nhb 0]]

That should do it.

On Feb 17, 2007, at 5:52 PM, alexandra.marques_at_fc.up.pt wrote:

> Hi
>
> I have a script to calculate the hydrogen bonds between some waters
> of the
> active site and the protein residues.However this script seems to
> work with
> trajectories but not with pdb files. The other problem is that I
> cannot obtain
> "the number of h-bonds in frame"; instead I obtain an output like
> this:
> number of h-bonds in frame 0: {19711 19711 19711}
> I am not seeing where the errors are in the script. Could someone
> please help
> me?
> Here is the script:
>
> set outfile [open "hbonds.out" w]
> set pep [atomselect top "protein"]
> set wat [atomselect top "water and ((within 4.0 of residue 0 to
> 254) and (within
> 4.0 of residue 255))"]
> set nf [molinfo top get numframes]
> for {set i 0} {$i < $nf} {incr i} {
> $pep frame $i
> $wat frame $i
> $pep update
> $wat update
> set nhb [measure hbonds 3.5 120 $wat $pep]
> puts ${outfile} "number of h-bonds in frame $i: $nhb"
> foreach donor [lindex $nhb 0] acceptor [lindex $nhb 1] {
> set seldonor [atomselect top "index $donor" frame $i]
> set donorResidue [$seldonor get residue]
> $seldonor delete
> set selacceptor [atomselect top "index $acceptor" frame $i]
> set acceptorResidue [$selacceptor get residue]
> $selacceptor delete
> puts "The donor has index $donor, belongs to residue $donorResidue"
> puts "The acceptor has index $acceptor, belongs to residue
> $acceptorResidue"
> puts ${outfile} "frame $i: donor mask :$donorResidue"
> puts ${outfile} "frame $i: acceptor mask :$acceptorResidue"
> }
> }
> close $outfile
>
> Thanks
> Alexandra
>
>
>
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