Hi AMBER,
To preface this and to give some extra information, I am analyzing an
inhibitor and protease in complex. PCA is extremely new information to me
and I do not have much prior knowledge ( I am still a novice at AMBER).
While following the tutorial on the AMBER website, the only changes I have
made were files names and types to match my data. All of my trajin files
are from the same simulation, not two different ones. I am not sure if this
matters or not, as the tutorial is comparing trajectories ran on a CPU vs
GPU (two different sims, not one like mine). Here are my terminal commands:
[alen2.itn2 16_complex]$ cpptraj
CPPTRAJ: Trajectory Analysis. V13.24
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
> parm complex_sol16.prmtop
AmberParm Title: [default_name]
Radius Set: H(N)-modified Bondi radii (mbondi2)
> trajin equil1.mdcrd parm
[equil1.mdcrd] contains 5000 frames.
> trajin equil2.mdcrd parm
[equil2.mdcrd] contains 5000 frames.
> trajin equil3.mdcrd parm
[equil3.mdcrd] contains 15000 frames.
> rms first :1-232&!.H=
RMSD: (:1-232&!.H*), reference is first frame (:1-232&!.H*), with
fitting.
> average crdset average16
AVERAGE: Averaging over coordinates in mask [*]
Start: 1 Stop: Final frame
Writing averaged coords to [crdset]
> createcrd trajectories16
CREATECRD: Saving coordinates from Top complex_sol16.prmtop to
"trajectories16"
> run
PARAMETER FILES:
0: complex_sol16.prmtop, 56822 atoms, 18004 res, box: Orthogonal, 17775
mol, 17762 solvent, 25000 frames
INPUT TRAJECTORIES:
0: [equil1.mdcrd] is an AMBER trajectory, Parm complex_sol16.prmtop
(Orthogonal box) (reading 5000 of 5000)
1: [equil2.mdcrd] is an AMBER trajectory, Parm complex_sol16.prmtop
(Orthogonal box) (reading 5000 of 5000)
2: [equil3.mdcrd] is an AMBER trajectory, Parm complex_sol16.prmtop
(Orthogonal box) (reading 15000 of 15000)
Coordinate processing will occur on 25000 frames.
REFERENCE COORDS:
No frames defined.
OUTPUT TRAJECTORIES:
No files.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM [complex_sol16.prmtop] (3 actions):
0: [rms first :1-232&!.H=]
Mask [:1-232&!.H*] corresponds to 1783 atoms.
1: [average crdset average16]
AVERAGE: Averaging over 56822 atoms.
2: [createcrd trajectories16]
----- [equil1.mdcrd] (1-5000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- [equil2.mdcrd] (1-5000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- [equil3.mdcrd] (1-15000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 25000 frames and processed 25000 frames.
ACTION OUTPUT:
AVERAGE: [crdset average16 ]
[crdset] is an AMBER trajectory, Parm complex_sol16.prmtop: Writing 25000
frames (1-Last, 1)
DATASETS:
2 data sets:
RMSD_00000 "RMSD_00000" (double), size is 25000
trajectories16 "trajectories16" (coords), size is 25000
complex_sol16.prmtop, 56822 atoms, 18004 res, box: Orthogonal, 17775 mol,
17762 solvent
> crdaction trajectories16 rms ref average16 :1-232&!.H=
Error: Could not get reference with name average16
Why am I getting "Error: Could not get reference with name average16"? The
files "average1" and "trajectories1" were not made within my directory,
only "crdset". Running the last command and replacing "average16" with
"crdset" returned the same error.
Furthermore, here is the complete list of commands that I modified from the
tutorial for my data, does this look correct moving forward?
cpptraj
parm complex_sol16.prmtop
trajin equil1.mdcrd parm
trajin equil2.mdcrd parm
trajin equil3.mdcrd parm
rms first :1-232&!.H=
average crdset average16
createcrd trajectories16
run
crdaction trajectories16 rms ref average16 :1-232&!.H=
crdaction trajectories16 matrix covar name covar16 :1-232&!.H=
runanalysis diagmatrix covar16 out evecs16.dat vecs 3 name myEvecs16 nmwiz
nmwizvecs 3 nmwizfile 16.nmd nmwizmask :1-232&!.H=
crdaction trajectories1 projection GPU modes myEvecs16 beg 1 end 3
:1-232&!.H= crdframes 16,last
hist GPU:1 bins 100 out hist16.agr norm name GPU-1
hist GPU:2 bins 100 out hist16.agr norm name GPU-2
hist GPU:3 bins 100 out hist16.agr norm name GPU-3
run
Any help or insight would be greatly appreciated.
Best Regards,
Alen
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Received on Tue Feb 12 2019 - 16:30:02 PST
