AMBER Archive (2009)

Subject: [AMBER] ptraj amber 10 file.

From: Catein Catherine (
Date: Wed Jun 10 2009 - 11:02:32 CDT

Dear Sir/Madam,


I did a MD calculation with explicit solvent and trying to interprete the results with ptraj. Here is the ptraj file that I used.


trajin ./md4.mdcrd.gz 1 1000 50
trajout md4_nobox.out nobox
reference ../test_water.inpcrd
rms reference out md4.rms @C1',N10
atomicfluct out md4.bfactor byres bfactor
average md4_average_nobox.pdb pdb nobox

This is what I found
rmsd is about 2.5 A.
bfactor is as high as 500 for some of the flexible residues, but about 50 for most of the protein residues.
water molecules were included in the average pdb file, even 'nobox' command was used
I found the manual included 'center' 'image' 'strip water' or 'nobox' commands. However, whenever, I include those keywords in the ptraj file, error of unexpected ' was found.
I am just wonder if I could like to estimate the rmsd, atomicfluct and average pdb files. Did my ptraj file do anything wrong?
I notes the rst and mdcrd files are very big, could you mind to command if the following setting are acceptable based on your experiences:
for a 100 ps MD (nstlim=50000, dt=0.002),
ntpr and ntwx = 100
and ntwr = 1000.
best regards,
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