Dear All,I would like to plot ligand rmsd and active site rmsd (residue 5A around bound ligand). I used the following script for calculating ligand rmsd through out simulation;parm complex.prmtop
trajin reimaged_complex.mdcrd
rms :536 first out lig-rmsd.dat
strip :WAT
strip :Na+job processed finely and got ligand rmsd plot, but I do not whether the above pasted script is correct or not. I have also tried to plot active site 5 angstroms rmsd using script pasted below;parm complex.prmtop
trajin reimaged_complex.mdcrd
rms first out 536-5ang.dat :536<:5.0&.CA,N,C
strip :WAT
strip :Na+But I got following errorzuh.node14:~/Working/sya/ptr1/4cm6/complex/min/equ/md> cpptraj -i 2.in
CPPTRAJ: Trajectory Analysis. V15.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 10/22/16 13:31:52
| Available memory: 266.293 MB
INPUT: Reading Input from file 2.in
[parm complex.prmtop]
Reading 'complex.prmtop' as Amber Topology
[trajin reimaged_complex.mdcrd]
Reading 'reimaged_complex.mdcrd' as Amber Trajectory
[rms first out 536-5ang.dat :536<:5.0&.CA,N,C]
Error: Tokenize: Wrong syntax [.]
Error: Tokenize: Wrong syntax [.]
RMSD: (:536<:5.0&.CA,N,C), reference is first frame (:536<:5.0&.CA,N,C), with fitting.
[strip :WAT]
STRIP: Stripping atoms in mask [:WAT]
[strip :Na+]
STRIP: Stripping atoms in mask [:Na+]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: 'complex.prmtop', 64964 atoms, 19480 res, box: Orthogonal, 18948 mol, 18930 solvent, 5000 frames
INPUT TRAJECTORIES:
0: 'reimaged_complex.mdcrd' is an AMBER trajectory, Parm complex.prmtop (Orthogonal box) (reading 5000 of 5000)
Coordinate processing will occur on 5000 frames.
TIME: Run Initialization took 0.0001 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'complex.prmtop' (3 actions):
0: [rms first out 536-5ang.dat :536<:5.0&.CA,N,C]
Error: Could not parse mask [:536<:5.0&.CA,N,C].
Warning: Setup failed for [rms first out 536-5ang.dat :536<:5.0&.CA,N,C]: Skipping
1: [strip :WAT]
Stripping 56790 atoms.
Stripped parm: 'complex.prmtop', 8174 atoms, 550 res, box: Orthogonal, 18 mol
2: [strip :Na+]
Stripping 12 atoms.
Stripped parm: 'complex.prmtop', 8162 atoms, 538 res, box: Orthogonal, 6 mol
----- reimaged_complex.mdcrd (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: 266.9376 s
TIME: Avg. throughput= 18.7310 frames / second.
ACTION OUTPUT:
DATASETS:
1 data set:
RMSD_00000 "RMSD_00000" (double, rms), size is 0
DATAFILES:
536-5ang.dat (Standard Data File): RMSD_00000
Warning: Set 'RMSD_00000' contains no data.
Warning: File '536-5ang.dat' has no sets containing data.
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 267.7264 seconds.
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
Theory Comput., 2013, 9 (7), pp 3084-3095.
Anyone can explain this to me please?
Best,
Saman Yousuf Ali
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Received on Sat Oct 22 2016 - 02:00:02 PDT
