[AMBER] RMS-fit during PCA

From: Anasuya Dighe <anasuya.mbu.iisc.ernet.in>
Date: Fri, 2 Sep 2016 15:08:31 +0530 (IST)

Dear Amber users,
 I am following the following link by Daniel Roe for carrying out PCA analysis :

http://amber.utah.edu/AMBER-workshop/London-2015/pca/pca-cpu-gpu.cpptraj

However, in spite of carrying out each step as shown in the tutorial, I am
facing an error when I execute these commands one by one on the cpptraj terminal
:

> parm 1abc_water.prmtop [apo]
> trajin ../1abc_wat_md1.crd.gz parm [apo]
> rms first :1-246&!.H=
> average crdset 1abc-average
> createcrd 1abc-trajectories
> run
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES:
 0: [apo] '1abc_water.prmtop', 34832 atoms, 10532 res, box: Orthogonal, 10287
mol, 10281 solvent, 5000 frames

INPUT TRAJECTORIES:
 0: '1abc_wat_md1.crd.gz' is an AMBER trajectory, Parm [apo] (Orthogonal box)
(reading 5000 of 5000)
  Coordinate processing will occur on 5000 frames.
TIME: Run Initialization took 0.0000 seconds.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '[apo]' (3 actions):
  0: [rms first :1-246&!.H=]
        Mask [:1-246&!.H*] corresponds to 1963 atoms.
        Mask [:1-246&!.H*] corresponds to 1963 atoms.
Warning: Coordinates are being rotated and box coordinates are present. Warning:
Unit cell vectors are NOT rotated; imaging will not be possible Warning: after
the RMS-fit is performed.
  1: [average crdset 1abc-average]
        Averaging over 34832 atoms.
  2: [createcrd 1abc-trajectories]
----- 1abc_wat_md1.crd.gz (1-5000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 5000 frames and processed 5000 frames.
TIME: Trajectory processing: 130.7463 s
TIME: Avg. throughput= 38.2420 frames / second.

ACTION OUTPUT:
    AVERAGE: [crdset 1abc-average]
        Writing 'crdset' as Amber Trajectory
  'crdset' is an AMBER trajectory, Parm [apo]: Writing 5000 frames (1-Last, 1)

DATASETS:
  2 data sets:
        RMSD_00000 "RMSD_00000" (double, rms), size is 5000
        1abc-trajectories "1abc-trajectories" (coordinates), size is 5000 (1993 MB) Box
Coords, 34832 atoms
---------- RUN END ---------------------------------------------------

>crdaction 1abc-trajectories rms ref 1abc-average :1-246&!.H=
Error: Could not get reference with name 1abc-average


When I enter the last command, i.e. fitting the frames to the average structure,
I am facing the errror message as shown above. I have already created crdset
1abc-average, then why isn't cpptraj able to get reference to 1abc-average when
calculating an rms fit ( in the last command ).

Any idea why this is happening? Am I going wrong somewhere?


Anasuya





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Received on Fri Sep 02 2016 - 03:00:02 PDT
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