AMBER Archive (2007)

Subject: AMBER: questions about analysing LES results

From: Kailee (kaileeamber_at_googlemail.com)
Date: Tue Jan 30 2007 - 11:00:40 CST

Dear all,

I am using LES method looking at diffusion of a gas molecule into a protein,
and I made 200 LES copies of that gas molecule.

Here is the general procedures how I did it:

The protein (residue 1 to 562) is first solvated using TIP3P water, and the
gas molecule is residue 563 (which was copied 200 times during the
production run). I minimized the system (non_LES) first, and heated it to
300K (non_LES as well), and then I used ADDLES program prepared the inputs
for LES sumulations, and then I ran sander.LES for the LES system.
Everything was fine, and I got .rst and .mdcrd outputs.

What I wanted is:
1st, I want to reimage the trajectories to the original box, and I used the
ptraj to do that, here is the script (reimage.ptraj):
################################################
trajin LES_md1.mdcrd
trajin LES_md2.mdcrd
trajout LES_12_reimage.mdcrd les split 200
center :1-562
image familiar
go
################################################
What I am not quite sure is: when I use 'center', should I use residue 1-562
which is only the protein, or 1-563 which includes the gas molecule?

2nd, I want to find out the diffusion pathway of the gas molecule. What I
did is I seperated my job into a few 100ps long smaller jobs, and I saved
the struture after every 100ps as PDB file and loaded them into VMD and
tried to superimpose them. Are there any better ways to do this? and also I
am not sure if I saved the PDB files correctly, as the gas molecule
coordinates looks really weird. And I used 'ambpdb' command to save the pdb
files like this:
$AMBERHOME/exe/ambpdb -p LES.prmtop <LES_md1.rst> LES_md1.pdb

Thank you all for reading my questions and any suggestion is welcome and
appreciated!

Kailee

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