Hi Christian,
It is often best to post to the AMBER mailing list (see
http://lists.ambermd.org/) since that way you will likely get a quicker
reply and others might be able to help better than me.
If I understand what you are saying. Right now you specify the dihedral in
ptraj and you get that dihedral as a function of time. However what you
actually want is all dihedrals for a given frame. Is that correct?
I am not sure there is an efficient way to do this in ptraj. It is designed
to process trajectories. One thing you could do is specify all of the
dihedrals as you have and tell ptraj to only read a single frame from the
trajectory. E.g.
trajin foo.netcdf 103 103 1
That way you would only get the one dihedral from that frame. You then cat
the output files together and repeat with frame 104 specified etc. This of
course would need to be scripted to be efficient. Beyond that you really
need something that transposes what is essentially a matrix for you. You
could use the paste command to paste all the individual columns together
into a single file representing a 2D matrix. This would give you time down
the file and dihedral across the file. The one could pipe this to tail to
get it to print you a specific row which you could write to a file giving
you a single file with the dihedrals for that specific time frame.
I hope that helps.
All the best
Ross
From: C. Parry [mailto:cspar07.gmail.com]
Sent: Tuesday, April 12, 2011 4:34 PM
To: Ross Walker
Subject: Coupled torsions from Amber
Hello Ross,
I am stomped by how to go about a task: I am able to get a series for a side
chain torsion chi1 from a long simulation. Likewise for chi2, ...,
Since I am trying to get some kind of a rotamer library I need to get {
chi1, chi2, chi3 ... }1, { chi1, chi2, chi3 ... }2, { chi1, chi2, chi3 ...
}3,... , fro very long time t. Could you please give me a clue how I may go
aboyut doing this.
I already have done something like this:
... ...
trajin /home/parrycs/Archive/m96/restore/cdb3_m96.98.netcdf
trajin /home/parrycs/Archive/m96/restore/cdb3_m96.99.netcdf
dihedral sp1_chi1 :41.N :41.CA :41.CB :41.SG out chi1-sp1_m96
dihedral sp1_chi2 :41.CA :41.CB :41.SG :41.S1 out chi2-sp1_m96
Thank you.
Christian Parry
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 12 2011 - 23:00:02 PDT
