AMBER Archive (2006)

Subject: Re: AMBER: hbond analysis

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Wed Oct 04 2006 - 09:49:35 CDT

Dear Vlad,

since you are presently studying h-bonds maybe you could answer this
question of mine. Do you know what is the meaning of the lifetime
parameter, the number after (in parenthesis) and of the maxocc
parameter, what are the units used for these three (or two since the
first two have the same units) parameters?

Thanks in advance!

Sergey

Vlad Cojocaru wrote:
> Dear Amber users,
>
> I am trying to use the ptraj hbond facility to analyze lifetimes of
> hydrogen bonds in a protein and between a protein and a ligand. More
> precisely, I am trying to define a set of donors and have ptraj printing
> out all Hbonds formed by these donors in at least 1 frame of the
> trajectory (with the donor-acceptor distance, angle, occupancy etc -
> see script below). However the output of this script is null. Maybe
> somebody can give me a hint what am I doing wrong here.
>
> I used to do this type of analysis with CARNAL and it always worked
> pretty nice but since now I am using ptraj for almost all analysis, I
> thought of using ptraj for this one as well. However, all the examples
> that I found an the amber archive were about solvent interactions in
> which the definition of donor and acceptors were exact.
>
> Best wishes
> vlad
>
>
> trajin file.mdcrd
> donor mask
> :47,76,78-84,94,192,193,216,260,264,268,336,361,468_at_NZ,N,NE,NH1,NH2,ND2,OG1
> acceptor mask :1-467_at_O* @H*
> hbond distance 3.2 angle 60.0 series hbonds.dat
> go
>
>

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