Hi,
On Sat, Jun 8, 2019 at 8:29 AM Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
>
> hbond H2 out HEM-hbond.out solventdonor :WAT solventacceptor :HEM,WAT.O
> avgout HEM-avg.dat solvout HEM-WATavg.dat bridgeout bridge-hb.out
This is close to what you want, but you should modify your masks a bit
and use the 'nointramol' keyword:
hbond H2 <protein/ligand mask> out HEM-hbond.out solventdonor :WAT
solventacceptor :WAT.O \
avgout HEM-avg.dat solvout HEM-WATavg.dat bridgeout bridge-hb.out nointramol
where <protein/ligand mask> selects your protein and heme (e.g.
':1-260,HEM'). The 'solventdonor' and 'solventacceptor' are for when
you have a bunch of similar molecules and you don't particularly care
which one is doing the hydrogen bonding (which is usually the case for
waters, ions, etc). The 'nointramol' keyword will tell 'hbond' to
avoid hydrogen bonds within the same molecule.
Hope this helps,
-Dan
> [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 Mon Jun 10 2019 - 06:00:06 PDT
