RE: AMBER: Average pdb

From: John Jett <>
Date: Thu, 23 Mar 2006 17:32:00 -0500

Hi Claire,

My thought is that you are getting the core dump before your script file
ever gets down to the strip line. I would think that it would core dump the
first time you input a trajin line that doesn't coordinate to your prmtop
file. You can test this theory by inputting the lines directly into ptraj
rather than using a script file. If it blows up when you trajin a line,
then there's your problem.

If that's the case I would try this. For your overall average, it seems
like you only care about creating a structure using the Calpha atoms of the
protein and not any of the ligands. What I would do is modify your five
average structures such that they only contain the Calpha atoms (doing so
one by one in ptraj) and then create a new topology which also contained
only the Calpha atom information. Then, you should be able to rerun ptraj
with these five new pdbs and one new top file.

Hope this helps!


>From: "Claire Zerafa" <>
>To: <>
>Subject: AMBER: Average pdb
>Date: Thu, 23 Mar 2006 22:17:33 +0100 (W. Europe Standard Time)
>Hi all,
>I have a question please. I am trying to fit the trajectory of a protein
>bound to 5 different ligands to an average pdb file. For each protein
>system, I have an average pdb file for the trajectory. Now I try to read
>each pdb file into ptraj and make an average pdb file out of those so that
>can fix each trajectory to the average pdb file to make it more
>representative of my system. My first question is as follows:
>For each of my 5 systems I have a prmtop file. When I come to run ptraj to
>generate the average pdb file do I just pick one of the prmtop files? Or is
>there a way of generating an average prmtop file?
>Second I created a script file as follows:
>Trajin /DATA/CORTICOSTERONE_pca_CA_only/corticosterone_average_output.pdb
>Trajin /DATA/METRIBOLONE_pca_CA_only/metribolone_average_output.pdb
>Trajin /DATA/UNDOCKED_pca_CA_only/UNDOCKED_average_output_ca.pdb
>Trajin /DATA/VINCLOZOLIN_pca_CA_only/vinclozolin_average_output.pdb
>Rms first out /DATA/all_av_rms1.out :.CA (GENERATES rms for the CA atoms
>Strip ~:.CA (STRIPS ALL BUT CA atoms- and therefore does away with any
>differences caused by presence of different ligands in pdb files)
>Average /DATA/all_av.pdb pdb nowrap (generates a pdb file containing only
>the CA atoms of the protein)
>I get a core dump. I can see why this happens ptraj expects a certain
>of atoms- specified by the prmtop file, and then finds a different amount-
>due to the different ligand size. I would have thought though, that since I
>am working only with the CA atoms of the protein, then this would not have
>mattered. How can I solve this please?
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Received on Sun Mar 26 2006 - 06:10:16 PST
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