Usually it's good to use the latest software. However, if you need to
recheck something done in Amber 9 or 10 or earlier software versions
it is good to remain within the framework of that software.
Just in case something might be different in the code or parameters of
newer versions.
To use ptraj you need to type:
ptraj name.top script.ptraj
ptraj calls for ptraj program
name.top is the topology of your .crd or .rst file
script.ptraj is the name of the script which has the name of your .crd
or .rst file along with the commands you want to use.
For amber 9 I used these scripts for ptraj
"Find average pdb structure"
trajin name.mdcrd
rms first :1-1772
average Average.pdb :1-1772 pdb
- here you can change to what you want to find average pdb. Will it be
backbone, certain atoms or all residues.
"This RMSD of your average pdb structure to your trajectory. In case
you need to find the closest (or most similar structure of your
trajectory to your average pdb) You will see that average pdb is all
"messed up" on some places so you can't really use it, but you can
find best fitting coordinates to it via this script"
trajin Average.pdb
trajin name.crd
reference Average.pdb
rms reference out rms-av.dat .CA,C,N
- here you can see that I was looking for rmsd on backbone atoms only
(ignoring positions of side chains of aminoacids or other molecules
and atoms presented. You can always use different approach here, like
use all residues :1-<number of your residues>
"If you ever need to get water closest to the certain residue for
certain applications this is the ptraj scrips I used. This script gets
you 1200 molecules of water nearest to the residue :1550 (if you used
.1550 that if you get you 1200 waters nearest to your atom 1550)
trajin name.rst
closestwater 1200 :1550
trajout wat.pdb pdb nobox
- however you can't use this script to get Na+ or other ions. That you
will have to do by hand if you want to. Or I just don't know more
effective way to do it.
These are all the scripts I have for old ptraj.
I think you can do a lot with them.
To get things closes to your residue use ambmask
/../amber9/exe/ambmask -p name.top -c name.rst -find ":1550<:30" > size30.pdb
This cuts out closest 30 angstroms to the :1550 residue (same thing
goes for . - if you need to use this for atoms)
/../amber9/exe/ambmask -p name.top -c name.rst -out -find ":1550<:60.7 &:Na+"
This gets you all Na+ residues around 60.7 angstroms of residue :1550
Citiram Mustafa Alhaji Isa <mustafaisa.unimaid.edu.ng>:
> Dear all,
>
> I am using amber 10, I want to perform analysis of RMSD, RMSF, Energy
> and other parameter using ptraj. Can someone help me with the script
> for performing the calculation
>
> --
> Warm regards
>
>
> Mustafa Alhaji Isa
> Bioinformatics and Computational BIology Lab,
> Department of Biotechnology,
> School of Engineering and Technology
> Sharda University
> Greater Noida, Delhi, India
> Mob No.: +918800621829
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jul 12 2017 - 01:30:02 PDT
