From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu May 31 2012 - 15:09:06 CDT

Don't try to guess what atoms are needed to form hbonds. Just make a relevant selection for your protein(s) or other molecules. Read the hbonds plugin webpage if its still not clear to you.

On May 31, 2012, at 1:00 PM, Subrata Paul wrote:

> In hbond plugin for water water hbobd
> selection1 name O
> and selection2 name O
> frams ALL
> selection1 is the Both
> distanec 3.4
> angle 60
> calculate details info for: all hbonds
>
> is this selection is ok?
> i am confused in selection and detais indormation.
> can you suggest me in this regard?
> it will be very grateful .
>
> is this possible to get hbond vs time?
>
> On Thu, May 31, 2012 at 9:34 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> Why not just use the hbonds plugin?
>
>
>
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Subrata Paul
> Sent: Thursday, May 31, 2012 10:40 AM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: hbonds vs time
>
>
>
> Dear sir
> I am simulating a water system in AMBER10 and want to calculate water-water hbonds.
> I have used followinf scrip in vmd tk console
>
> set outfile [open numHbonds.dat w]
> set numframes [molinfo top get numframes]
> set cutoff 3.4
> set angle 60
> set sel1 [atomselect top "name O"]
> set sel2 [atomselect top "name O"]
> for {set i 0} {$i < $numframes} {incr i} {
> $sel1 frame $i
> $sel2 frame $i
> puts $outfile "[measure hbonds $cutoff $angle $sel1 $sel2]"
> }
> close $outfile
>
> Is there my selection is ok??
>
> I have attache d the out file but do not understand the out file?
>
> what should be scripts for hbond vs time?
>
> with appreciate
> --
> With Best Regards
> Subrata
> PhD Student
> Dept of Chemistry.
> IIT G
>
>
>
>
>
> --
> With Best Regards
> Subrata
> PhD Student
> Dept of Chemistry.
> IIT G
>
>