AMBER Archive (2005)

Subject: AMBER: RE: tutorial 8

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jun 22 2005 - 16:15:33 CDT

Hi Xeuping,

> I have some question regarding tutorial 8. The ptraj
> script for hydrogen bond analysis:
> analyse_hbond.ptraj, does it apply to all the protein?
> (besides the backbone donor and acceptor that we need
> to modified according to my protein).

Yes it should do. At least it should apply to all the standard amino acids
in a protein. If you have any non standard residues you have built yourself
(or DNA bases etc) you will need to add the donor and acceptors for these to
the list. Bare in mind this script was created in a bit of a hurry for a
workshop so there may be some things missing. Although I think it is
complete. Let me know if you see anything obvious that is missing.

> I don't really understand the result, what is the
> lifetime maxocc columm indicate? can u please explain
> to me? Is there any easier way to present the result
> data? (in graph or table?)

I don't know if there is an easier way to present the results take a look at
the ptraj section of the manual, there may be a more verbose way to output
the data.

I'm not entirely sure what the numbers under maxocc / lifetime represent
(units?) perhaps someone on the amber mailing list can comment further here.
The little bar graph with the symbols at the far right of the output tells
you in what section of the trajectory this H bond is detected and for how
much of that section it is present. E.g. In this case there are 10 columns
so each column represents 5ns of the simulation. A "o" means that during
that 5ns this H bond was present 40 to 60% of the time.

> I am doing MD simulation on protein at two different
> temperature, i was thinking to look at the changes of
> hydrogen bonding in two different temperature. This
> tutorial has give me some ideas, thank you very much.

You are welcome.
 
> lastly, do you have any idea how to do analysis of rms
> vs residue?

I have done this with Carnal - here is an example script:

FILES_IN
  PARM p1 1LDY_Charmm_Pavelites_NICH_full_params.prmtop;
  STATIC t1 1LDY_Charmm_Pavelites_NICH_full_params.prmcrd;
  STREAM s1 ../1LDY_Pavelites_NICH_Full_prod_300K_10ps.mdcrd.bz2;

FILES_OUT
  TABLE tab1 1LDY_pav_full_rms_per_res_1_to_756.tab;
  
DECLARE
  GROUP solute (RES 1-756);
  RMS fit1 FIT solute s1 t1;
  
OUTPUT
  TABLE tab1 fit1%residues;
 
END

This gives you a lot of data, RMS fits vs time for each residue and also in
the carnal output file and average RMS for each residue. You can probably do
a similar thing with ptraj, I haven't looked into it though.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

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