AMBER: problem with ptraj

From: Terry Lang <>
Date: Mon, 24 Sep 2007 15:55:29 -0700

Hey Everyone,

       I am currently trying to compare the effect of explicit solvent
vs GB on a simulation of a protein. In addition to the more commonly
used RMSD comparison, we also have experimental FRET data that I am
including in the analysis. I have used leap to create both parameter
and coordinate files (and solvent and ions for the explicit solvent
model). Using an external program, I found that all-atom RMSD between
the parameter and coordinate files prepared for the GB simulation to be
0.0 RMSD from the explicit solvent files, which is what I would expect.
However, when I use ptraj to compute the distances to get a starting
value for the FRET analysis, I get really different answers between the
GB and exp solvent structures (different by 2.5 A for one distance and
almost 5 A for the other). This difference is really concerning as we
are looking for changes in FRET in response to changes in the protein
and this discrepancy really affects our evaluation. It also makes me
very concerned that the rest of the distance data is not reliable for
either simulation.
    I am using the following scripts to generate the data:


ptraj prot.prm << EOF
trajin prot.crd
distance fret1 :202 :255 out dist_fret1_exp.txt
distance fret2 :217 :255 out dist_fret2_exp.txt
distance fret3 :200 :255 out dist_fret3_exp.txt


ptraj prot_gb.prm << EOF
trajin prot_gb.crd
distance fret1 :202 :255 out dist_fret1_gb.txt
distance fret2 :217 :255 out dist_fret2_gb.txt
distance fret3 :200 :255 out dist_fret3_gb.txt

NOTE: I have also tried this comparison with water, hydrogens and
sodium ions stripped but found no difference.

Any thoughts on what I am doing wrong? I am using AMBER 9 patched
through bugfix.31 on Debian.


P. Therese Lang
Post Doc
Alber Lab, UC Berkeley
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Received on Wed Sep 26 2007 - 06:07:08 PDT
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