Dear All,
I am a bit confused about the exact usage of hbond command that will give
me all hbonds that ligand (HEM) makes irrespective of whether they are
with backbone, side-chain or waters or are via bridging waters.
I have used the following inputs but not sure if it is doing the right
thing.
The output file contains all hbonds (a large number of which I'm not
interested to find at present).
Please suggest me on how to give correct mask for all protein residues
which will be searched for h-bond with ligand and bridges to ligand via
waters.
thanks a lot.
[r11831vd.hlogin2 [csf3] 3A4-explicit-sol]$ more hbond-1.inp
parm P450-1W0E.prmtop
trajin P450-1W0E-equilpH45.nc
hbond H2 out HEM-hbond.out solventdonor :WAT solventacceptor :HEM,WAT.O
avgout HEM-avg.dat solvout HEM-WATavg.dat bridgeout bridge-hb.out
[r11831vd.hlogin2 [csf3] 3A4-explicit-sol]$ cpptraj hbond-1.inp
Warning: Assuming 'hbond-1.inp' contains cpptraj input.
CPPTRAJ: Trajectory Analysis. V4.14.0 (AmberTools V19.02)
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 06/08/19 13:19:04
| Available memory: 3.868 GB
INPUT: Reading input from 'hbond-1.inp'
[parm P450-1W0E.prmtop]
Reading 'P450-1W0E.prmtop' as Amber Topology
Radius Set: H(N)-modified Bondi radii (mbondi2)
[trajin P450-1W0E-equilpH45.nc]
Reading 'P450-1W0E-equilpH45.nc' as Amber NetCDF
[hbond H2 out HEM-hbond.out solventdonor :WAT solventacceptor :HEM,WAT.O
avgout HEM-avg.dat solvout HEM-WATavg.dat bridgeout bridged-hb.out]
HBOND: Searching for Hbond donors/acceptors in region specified by *
Will search for hbonds between solute and solvent donors in [:WAT]
Will search for hbonds between solute and solvent acceptors in
[:HEM,WAT.O]
Distance cutoff = 3.000, Angle Cutoff = 135.000
Writing # Hbond v time results to HEM-hbond.out
Writing Hbond avgs to HEM-avg.dat
Writing solute-solvent hbond avgs to HEM-WATavg.dat
Writing solvent bridging info to bridged-hb.out
Solvent bridges will be determined between solute residues.
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: P450-1W0E.prmtop, 49762 atoms, 14475 res, box: Trunc. Oct., 14003 mol,
14000 solvent
INPUT TRAJECTORIES (1 total):
0: 'P450-1W0E-equilpH45.nc' is a NetCDF AMBER trajectory with coordinates,
time, box, Parm P450-1W0E.prmtop (Trunc. Oct. box) (reading 500 of 500)
Coordinate processing will occur on 500 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'P450-1W0E.prmtop' (1 actions):
0: [hbond H2 out HEM-hbond.out solventdonor :WAT solventacceptor
:HEM,WAT.O avgout HEM-avg.dat solvout HEM-WATavg.dat bridgeout
bridged-hb.out]
Acceptor-only atoms: 664
Donor/acceptor sites: 657
Donor-only sites: 0
815 solute hydrogens.
Solvent sites (14000)
28000 solvent hydrogens, 0 ions.
Estimated max potential memory usage: 1.433 GB
----- P450-1W0E-equilpH45.nc (1-500, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 500 frames and processed 500 frames.
TIME: Avg. throughput= 11.0011 frames / second.
ACTION OUTPUT:
HBOND: Actual memory usage is 207.660 kB
1317 solute-solute hydrogen bonds.
627 solute-solvent hydrogen bonds.
520 unique solute-solvent bridging interactions.
TIME: Analyses took 0.0000 seconds.
DATASETS (4 total):
H2[UU] "H2[UU]" (integer), size is 500 (2.000 kB)
H2[UV] "H2[UV]" (integer), size is 500 (2.000 kB)
H2[Bridge] "H2[Bridge]" (integer), size is 500 (2.000 kB)
H2[ID] "H2[ID]" (string), size is 500 (232.194 kB)
Total data set memory usage is at least 238.194 kB
DATAFILES (4 total):
HEM-hbond.out (Standard Data File): H2[UU] H2[UV] H2[Bridge] H2[ID]
HEM-avg.dat (Avg. solute-solute HBonds)
HEM-WATavg.dat (Avg. solute-solvent HBonds)
bridged-hb.out (Solvent bridging info)
RUN TIMING:
TIME: Init : 0.0001 s ( 0.00%)
TIME: Trajectory Process : 45.4499 s ( 99.95%)
TIME: Action Post : 0.0090 s ( 0.02%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0143 s ( 0.03%)
TIME: Other : 0.0008 s ( 0.00%)
TIME: Run Total 45.4742 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 45.6328 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.
[r11831vd.hlogin2 [csf3] 3A4-explicit-sol]$
--
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 Jun 08 2019 - 05:30:02 PDT
