Re: [AMBER] Generating an average structure from a rst/pdb list?

From: Baptiste Legrand <>
Date: Thu, 03 Mar 2011 22:02:04 +0100

Le 03/03/2011 19:54, Daniel Roe a écrit :
> Hi,
> On Thu, Mar 3, 2011 at 12:21 PM, Baptiste Legrand<> wrote:
>> I have first tried to trajin all my rst but it seems that only the first
>> file is taken in account:
> How do you know only the first file is taken into account (are there
> error messages etc)?
>> So in a second stage, I have concatenated with the cat command and then
>> launch the my traj script:
> You can't concatentate restart files - by design they contain only one
> set of coordinates (and optionally velocities). Only the first set
> will be read.
>> Checking coordinates: all.rst
>> readAmberRestart(): topology/coordinates file are inconsist with
>> NATOMS = 1138 (1248)
> This indicates that the number of atoms in your topology does not
> match the number of atoms in the restart file, I suspect as a result
> of the 'STRIP :CL3'. You would need to generate a new topology file
> without :CL3 in order to process files stripped of :CL3.
> -Dan
> _______________________________________________
> AMBER mailing list
Thanks, indeed I used the bad topology files. This new script works
fine. I have just a problem with the "average average.rst rest" which
generates an empty rst file...

for x in `seq 1 20`
cat > trajin <<EOF
trajin C70_$x.rst
trajout C70s_$x.rst
ptraj ../prep/C70_$x.prmtop < trajin
cat > trajin <<EOF
trajin C70s_1.rst
trajin C70s_2.rst
rms first mass out .N1,C9,C11,N2,C12,C17,C20,N3,C21,C29,N4
image center familiar
average average.pdb pdb
average average.rst rest
ptraj C70.prmtop < trajin
#sander -O -i -o C70.out -c average.rst -p C70.prmtop -r C70mean.rst

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Received on Thu Mar 03 2011 - 13:30:02 PST
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