AMBER Archive (2006)

Subject: Re: AMBER: hbond analysis

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed Oct 04 2006 - 10:26:32 CDT

Dear Sergey,

I was only trying to do an Hbond analysis with ptraj but it seems that
ptraj doesn't really do what I would like it to do. So, I decided to do
the analysis with CARNAL and more recently (as of today actually) with
VMD. So, I didn't yet analyze ptraj outputs from Hbond analysis ...
Although I might have a guess of what these parameters mean, I would
rather let somebody else with more experience answer you.

Best
vlad

Sergey Samsonov wrote:

> 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
>>
>>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu