Dear Amber users and experts,
I want to write pdb files with charges.
Thus I'm trying to use cpptraj as shown below, but to my surprise no pdb
files are written and there is no error message to troubleshoot.
Can you please help me understand the correct combination of options to
make this work?
I'm using Amber18/AmberTools18.
Cpptraj input file: traj-pqr-cpptraj.in
parm 4ZF6_solv.prmtop
trajin 4ZF6_solv-prod300.nc 1 200
strip :WAT #:Cl- :NA+
trajout 4ZF6_solv.pdb pdb multi nobox dumpq onlyframes 0,49,99
Cpptraj output on the terminal
[user.localhost MD-4ZF6-3--15]$ cpptraj -i traj-pqr-cpptraj.in
CPPTRAJ: Trajectory Analysis. V4.14.0 (AmberTools V19.11)
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 10/04/20 09:59:54
| Available memory: 36.464 GB
INPUT: Reading input from 'traj-pqr-cpptraj.in'
[parm 4ZF6_solv.prmtop]
Reading '4ZF6_solv.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
[trajin 4ZF6_solv-prod300.nc 1 200]
Reading '4ZF6_solv-prod300.nc' as Amber NetCDF
[strip :WAT ]
STRIP: Stripping atoms in mask [:WAT]
[trajout 4ZF6_solv.pdb pdb multi nobox dumpq onlyframes 0,49,99]
Saving frames 0 49 99
Writing '4ZF6_solv.pdb' as PDB
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: 4ZF6_solv.prmtop, 61611 atoms, 18513 res, box: Orthogonal, 18052 mol,
18037 solvent
INPUT TRAJECTORIES (1 total):
0: '4ZF6_solv-prod300.nc' is a NetCDF AMBER trajectory with coordinates,
time, box, Parm 4ZF6_solv.prmtop (Orthogonal box) (reading 200 of 2000)
Coordinate processing will occur on 200 frames.
OUTPUT TRAJECTORIES (1 total):
'4ZF6_solv.pdb' (200 frames) is a PDB file (1 file per frame), writing
charges to occupancy column and GB radii to B-factor column no box info,:
Writing frames 0 49 99
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '4ZF6_solv.prmtop' (1 actions):
0: [strip :WAT ]
Stripping 54111 atoms.
Stripped topology: 7500 atoms, 476 res, box: Orthogonal, 15 mol
.....................................................
ACTIVE OUTPUT TRAJECTORIES (1):
4ZF6_solv.pdb (coordinates, time)
----- 4ZF6_solv-prod300.nc (1-200, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 200 frames and processed 200 frames.
TIME: Avg. throughput= 490.0916 frames / second.
ACTION OUTPUT:
TIME: Analyses took 0.0000 seconds.
RUN TIMING:
TIME: Init : 0.0001 s ( 0.02%)
TIME: Trajectory Process : 0.4081 s ( 99.69%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0012 s ( 0.00%)
TIME: Run Total 0.4094 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.6527 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.
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Sat Oct 03 2020 - 22:00:02 PDT
