AMBER Archive (2006)

Subject: AMBER: use ptraj and two differenct prmtop file to analyze LES trajectory

From: pang zhao (zhao.pang_at_gmail.com)
Date: Fri Jun 09 2006 - 03:56:57 CDT

Dear All,

I use leap.top to generate the les input file les.top. The 200 ps NPT LES
simulation generate the npt.mdcrd with a size of about 400 M,

This trajectory can be analyzed using ptraj module in amber 9 with les.top.
My ptraj input file:
trajin npt.mdcrd
center :1-342 origin mass
image origin center familiar
rms first out les_rms.out :1-342_at_CA
trajout les.mdcrd les split

For ptraj module in amber 9, its usage :
trajout filename [ format ] [ nobox ] [little | big] [dumpq | parse]
[nowrap] [les split|average]
LES support: The optional keyword "les" is used for the analysis of LES
trajectory.
The option "split" will output P separate trajectories, one for each LES
group (P is
copy number).

I have 5 copy and just copy the ligand 343,Acoording to the manual, ptraj
shoud output 5 separate trajectories(here P = 5), but ptraj just trajout
only one single trajectory les.mdcrd with a size about 2G. I guess that the
five trajectory may be intergrated into one. Acoording to the manual, ptraj
shoud output 5 separate trajectories

What is intersting is that,
Using ptraj, the les,mdcrd can be analyzed with two differenct top file,
leap.top, les.top. But the coordinates of output pdb files are different.

Looking forward to any suggestions.

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