Re: AMBER: problem with ptraj

From: Carlos Simmerling <>
Date: Mon, 24 Sep 2007 20:45:44 -0400

you might want to use ptraj to calc the rmsd as well, to see if it
also matches or if perhaps there is some problem in reading the files.

ptraj should list the number of atoms in each mask- do they match?
your ptraj input sure looks like you should get the same results,
but if you don't then something is wrong probably not involving ptraj.

On 9/24/07, Terry Lang <> wrote:
> 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:
> #!/bin/csh
> 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
> #!/bin/csh
> 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.
> Sincerely,
> Terry
> --
> P. Therese Lang
> Post Doc
> Alber Lab, UC Berkeley
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Received on Wed Sep 26 2007 - 06:07:09 PDT
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