Dear All,
While trying to convert trajectory from nc to mdcrd format I'm getting the
following warnings about these I'm not able to find much useful information
by Googling or searching cpptraj page (
https://amber-md.github.io/cpptraj/CPPTRAJ.xhtml).
Thus please help me in understanding if it is ok to ignore these.
Thank you.
(base) [exx.c107739 Cytb5-Fe2-Hb-Fe3]$ cpptraj
CPPTRAJ: Trajectory Analysis. V4.25.6
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 12/17/20 19:51:16
| Available memory: 30.756 GB
> parm 1hga-3ner-solv.prmtop
[parm 1hga-3ner-solv.prmtop]
Reading '1hga-3ner-solv.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
Warning: Amber topology flag 'CMAP_COUNT' is unrecognized and will be
skipped.
Warning: Amber topology flag 'CMAP_RESOLUTION' is unrecognized and will be
skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_01' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_02' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_03' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_04' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_05' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_06' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_07' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_08' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_09' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_10' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_11' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_12' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_13' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_14' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_INDEX' is unrecognized and will be
skipped.
> trajin 1hga-3ner-solv-prod300.nc
[trajin 1hga-3ner-solv-prod300.nc]
Reading '1hga-3ner-solv-prod300.nc' as Amber NetCDF
> trajout 1hga-3ner-solv-prod300.mdcrd
[trajout 1hga-3ner-solv-prod300.mdcrd]
Warning: Format not specified and extension '.mdcrd' not recognized.
Defaulting to Amber Trajectory.
Writing '1hga-3ner-solv-prod300.mdcrd' as Amber Trajectory
> quit
[quit]
There are actions/analyses/trajectories queued. Really quit? [y/n]> n
> run
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: 1hga-3ner-solv.prmtop, 43800 atoms, 13605 res, box: Orthogonal, 13372
mol, 13363 solvent
INPUT TRAJECTORIES (1 total):
0: '1hga-3ner-solv-prod300.nc' is a NetCDF AMBER trajectory with
coordinates, time, box, Parm 1hga-3ner-solv.prmtop (Orthogonal box)
(reading 2000 of 2000)
Coordinate processing will occur on 2000 frames.
OUTPUT TRAJECTORIES (1 total):
'1hga-3ner-solv-prod300.mdcrd' (2000 frames) is an AMBER trajectory
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTIVE OUTPUT TRAJECTORIES (1):
1hga-3ner-solv-prod300.mdcrd (coordinates, time, box)
----- 1hga-3ner-solv-prod300.nc (1-2000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70%
--
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
P Please consider the environment before printing this e-mail
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Received on Thu Dec 17 2020 - 07:00:02 PST
