AMBER Archive (2009)

Subject: Re: [AMBER] HB for each snapshot

• Previous message: steinbrt_at_rci.rutgers.edu: "Re: [AMBER] RE: question"
• In reply to: Marcin Krol: "[AMBER] HB for each snapshot"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

Marcin Krol a écrit :
> Hello,
>
> A couple of weeks ago I asked whether ptraj can tell me the presence
> or absence of HB for each snapshot of a trajectory between a given
> pair of residues. Using hbond facility I can get occupancy and a
> graphical representation showing schematic of time-series, but what I
> really need is the HB information for each snapshot. I'm sure ptraj
> generates this info (to get the occupancy, etc), but I don't know how
> to get it. Please let me know i if I can get _per snaphot_ analysis of
> HBs in ptraj, it'll save me lots of work.
>
> Or maybe you can suggest another program to perform such analysis. Any
> help appreciated
Hello,

It is relatively straightforward to calculate the number of H bonds with
VMD.

Cheers,
Nicolas

>
> Thanks in advance
> best
> Marcin
>

• text/x-vcard attachment: nicolas_sapay.vcf

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

• Previous message: steinbrt_at_rci.rutgers.edu: "Re: [AMBER] RE: question"
• In reply to: Marcin Krol: "[AMBER] HB for each snapshot"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]