Hello Amber Users & Developers,
I have been attempting to analyze water-mediated hydrogen bonding between a ligand and protein residues. I understand that the hbond bridgeout command should be able to do this. However, my attempts to use the command have been unsuccessful. I can only get hbond information using the out command (solute-solute Hbond (aspect [UU])) and avgout. No information will print out for solvout (aspect [UV]) or bridgeout (aspect [Bridge]).
Cpptraj is updated to V13.0
I've been trying to run this command on my solvated trajectory file:
hbond out Hbond.dat avgout Avg.dat solvout Solv.dat bridgeout Bridge.dat
(I've also tried hbond bridgeout Bridge.dat)
This is the cpptraj output. The lack of info about the solvout and brideout commands in lines 16-17 indicates to me that the commands aren't being read.
----------------------------------------------------------------------------------------------
CPPTRAJ: Trajectory Analysis. V13.0
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
AmberParm Title: [default_name]
Radius Set: modified Bondi radii (mbondi)
INPUT: Reading Input from file test.in
[parm /mnt/hi/Documents/churchil/Laulimalide-April-2013/production-1/MT-LA-truncated-sol.prmtop]
Warning: Parm /mnt/hi/Documents/churchil/Laulimalide-April-2013/production-1/MT-LA-truncated-sol.prmtop already loaded, skipping.
[trajin /mnt/hi/Documents/churchil/Laulimalide-April-2013/production-1/analysis/cpptraj-combine/combined-solv-traj.mdcrd.nc 1 10 1 ]
[combined-solv-traj.mdcrd.nc] contains 675015 frames.
[hbond out Hbond.dat avgout Avg.dat solvout Solv.dat bridgeout Bridge.dat]
HBOND: Searching for Hbond donors/acceptors in region specified by *
Distance cutoff = 3.000, Angle Cutoff = 135.000
Dumping # Hbond v time results to Hbond.dat
Dumping Hbond avgs to Avg.dat
PARAMETER FILES:
0: MT-LA-truncated-sol.prmtop, 295649 atoms, 91601 res, box: Trunc. Oct., 89877 mol, 89452 solvent, 10 frames
INPUT TRAJECTORIES:
0: [combined-solv-traj.mdcrd.nc] is a NetCDF AMBER trajectory, Parm MT-LA-truncated-sol.prmtop (Trunc. Oct. box) (reading 10 of 675015)
Coordinate processing will occur on 10 frames.
REFERENCE COORDS:
No frames defined.
OUTPUT TRAJECTORIES:
No files.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM [MT-LA-truncated-sol.prmtop] (1 actions):
0: [hbond out Hbond.dat avgout Avg.dat solvout Solv.dat bridgeout Bridge.dat]
Set up 94447 acceptors:
Set up 181862 donors:
----- [combined-solv-traj.mdcrd.nc] (1-10, 1) -----
0% 11% 22% 33% 44% 56% 67% 78% 89% 100% Complete.
Read 10 frames and processed 10 frames.
ACTION OUTPUT:
DATASETS:
1 data set:
HB_00000[UU] "HB_00000[UU]" (integer), size is 10
DATAFILE OUTPUT:
Hbond.dat: HB_00000[UU]
Hbond.dat: Writing 10 frames.
----------------------------------------------------------------------------------------------
Does anyone have any ideas on what the problem may be? Thank you, in advance, for your time.
Sincerely,
Cassandra Churchill
PhD Student
Department of Chemistry
University of Alberta
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Received on Tue Jul 16 2013 - 10:00:03 PDT
