Dear AMBER experts,
Following the AMBER 20 tutorial “6.3 Using Accelerated Molecular Dynamics (aMD) to enhance sampling” I have conducted production MD simulation of my protein. Unfortunately, I have faced problems attempting to analyze the MD simulation results by the cpptraj input file presented in the chapter 3) Analyzing the aMD results
https://ambermd.org/tutorials/advanced/tutorial22/section3.php
of the tutorial.
The tutorial used to produce the PCA vectors from the aMD trajectory and further project this trajectories onto the produced PCA vectors.
I have adopted the original cpptraj input to the number of residues 748 in my protein.
It seems that the cpptraj input file in the tutorial contains obsolete commands.
See Warning reports in the OUT file below.
I need your help to resolve the problem.
Thank you,
Michael
The command line to run the aMD_post_process_ptraj.in file through cpptraj is the following:
cpptraj < aMD_post_process_ptraj.in > aMD_post_process_ptraj.out
aMD_post_process_ptraj.in
parm ../mc.prmtop
trajin ../7_/md_prod_amd0.mdcrd 1 last 1
reference ../6_/eq.rst
center origin :1-748
image origin center
strip :WAT,Cl-,Na+
rms reference mass :1-748.CA,C,N out aMD_0_RMSD.out
matrix covar name matrixdat .CA out covmat-ca.dat
analyze matrix matrixdat out evecs-ca.dat vecs 2244
analyze matrix matrixdat name evecs-ca vecs 2244
analyze modes fluct out analyzemodesflu.dat stack evecs-ca beg 1 end 2244
analyze modes displ out analyzemodesdis.dat stack evecs-ca beg 1 end 2244
projection modes evecs-ca.dat out pca12-ca beg 1 end 3 .CA
go
aMD_post_process_ptraj.out
CPPTRAJ: Trajectory Analysis. V4.25.6 (AmberTools V20.11)
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 09/15/21 15:20:08
| Available memory: 2.005 GB
INPUT: Reading input from 'STDIN'
[parm ../mc.prmtop]
Reading '../mc.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
[trajin ../7_/md_prod_amd0.mdcrd 1 last 1]
Reading '../7_/md_prod_amd0.mdcrd' as Amber NetCDF
[reference ../6_/eq.rst]
Reading '../6_/eq.rst' as Amber NC Restart
Setting active reference for distance-based masks: 'eq.rst'
[center origin :1-748]
CENTER: Centering coordinates using geometric center of atoms in mask (:1-748) to
coordinate origin.
[image origin center]
IMAGE: By molecule to origin based on center of mass using all atoms
[strip :WAT,Cl-,Na+]
STRIP: Stripping atoms in mask [:WAT,Cl-,Na+]
[rms reference mass :1-748.CA,C,N out aMD_0_RMSD.out]
RMSD: (:1-748.CA,C,N), reference is "default_name" (:1-748.CA,C,N), mass-weighted.
Best-fit RMSD will be calculated, coords will be rotated and translated.
[matrix covar name matrixdat .CA out covmat-ca.dat]
MATRIX: Calculating covariance matrix, output is by atom.
Printing to file covmat-ca.dat
Matrix data set is 'matrixdat'
Start: 1 Stop: Final frame
Mask1 is '.CA'
[analyze matrix matrixdat out evecs-ca.dat vecs 2244]
Warning: The 'analyze' prefix is no longer necessary and may be soon deprecated.
Warning: NOTE: 'analyze matrix' is now 'diagmatrix'.
Changed DataFile 'evecs-ca.dat' type to Evecs file for set Modes_00004
DIAGMATRIX: Diagonalizing matrix matrixdat and writing modes to evecs-ca.dat
Calculating 2244 eigenvectors.
Storing modes with name: Modes_00004
[analyze matrix matrixdat name evecs-ca vecs 2244]
Warning: The 'analyze' prefix is no longer necessary and may be soon deprecated.
Warning: NOTE: 'analyze matrix' is now 'diagmatrix'.
DIAGMATRIX: Diagonalizing matrix matrixdat
Calculating 2244 eigenvectors.
Storing modes with name: evecs-ca
[analyze modes fluct out analyzemodesflu.dat stack evecs-ca beg 1 end 2244]
Warning: The 'analyze' prefix is no longer necessary and may be soon deprecated.
Warning: To add an analysis command the the queue, only the command name needs
Warning: to be specified, e.g. 'modes <args>'.
Warning: Argument 'stack' is deprecated, use 'name <modes>' instead.
ANALYZE MODES: Calculating rms fluctuations using modes from evecs-ca, modes 1 to 2244
Results are written to 'analyzemodesflu.dat'
Boltzmann statistics used.
Eigenvectors associated with zero or negative eigenvalues will be skipped.
[analyze modes displ out analyzemodesdis.dat stack evecs-ca beg 1 end 2244]
Warning: The 'analyze' prefix is no longer necessary and may be soon deprecated.
Warning: To add an analysis command the the queue, only the command name needs
Warning: to be specified, e.g. 'modes <args>'.
Warning: Argument 'stack' is deprecated, use 'name <modes>' instead.
ANALYZE MODES: Calculating displacements using modes from evecs-ca, modes 1 to 2244
Results are written to 'analyzemodesdis.dat'
Boltzmann statistics used.
Eigenvectors associated with zero or negative eigenvalues will be skipped.
Factor for displacement: 1.000000
[projection modes evecs-ca.dat out pca12-ca beg 1 end 3 .CA]
Warning: Set 'RMSD_00002' contains no data.
Warning: File 'aMD_0_RMSD.out' has no sets containing data.
Warning: Set 'matrixdat' contains no data.
Warning: File 'covmat-ca.dat' has no sets containing data.
Warning: Set 'Modes_00004' contains no data.
Warning: File 'evecs-ca.dat' has no sets containing data.
Warning: Set 'FLUCT_00006[rmsX]' contains no data.
Warning: Set 'FLUCT_00006[rmsY]' contains no data.
Warning: Set 'FLUCT_00006[rmsZ]' contains no data.
Warning: Set 'FLUCT_00006[rms]' contains no data.
Warning: File 'analyzemodesflu.dat' has no sets containing data.
Warning: Set 'DISPL_00010[displX]' contains no data.
Warning: Set 'DISPL_00010[displY]' contains no data.
Warning: Set 'DISPL_00010[displZ]' contains no data.
Warning: File 'analyzemodesdis.dat' has no sets containing data.
TIME: Total execution time: 0.4572 seconds.
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
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Received on Wed Sep 15 2021 - 06:00:02 PDT
