AMBER Archive (2006)

Subject: AMBER: Average pdb

From: Claire Zerafa (
Date: Thu Mar 23 2006 - 15:17:33 CST

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 ligand
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 I
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 number
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?



The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to