Best Regards,
Baig Abdullah Al Muhit
PhD student/Graduate Teaching Assistant
Department of Civil and Environmental Engineering
School of Engineering
Vanderbilt University, Nashville, TN
________________________________________
From: Al Muhit, Baig Abdullah
Sent: Friday, July 14, 2017 3:03 PM
To: amber.ambermd.org
Subject: hbond analysis with CPPTRAJ
Hello everyone,
I am new to AMBER. I installed AmberTools-17 in CenTOS. I want to calculated h-bonds between two water molecules using CPPTRAJ. This is what I did:
1. I collected wat.dat and coord.dcd file from LAMMPS simulation.
2. Then I used VMD to convert wat.dat to wat.pdb file. Here's how the pdb file looks like:
CRYST1 6.649 3.325 3.325 90.00 90.00 90.00 P 1 1
ATOM 1 O1 1 HOH 1 0.051 0.866 -0.474 0.00 0.00
ATOM 2 H1 1 HOH 1 0.158 0.001 -0.304 0.00 0.00
ATOM 3 H2 1 HOH 1 -0.065 1.048 -1.338 0.00 0.00
ATOM 4 O2 2 HOH 2 3.378 -0.739 1.189 0.00 0.00
ATOM 5 H3 2 HOH 2 3.287 -1.604 1.374 0.00 0.00
ATOM 6 H4 2 HOH 2 3.460 -0.570 0.322 0.00 0.00
END
3. I used pdb as topology file and .dcd as coordinate file in AMBER using:
parm wat.pdb
trajin coord.dcd
It says
Warning: wat.pdb: Determining default bond distances from element types.
But, I realize it's because of how PDB files are set up.
4. Then I calculated the hydrogen bonds using this command:
hbond All :1-2 distance 4.5 out hbond.dat
5. Run the analysis
But the output says:
0 solute-solute hydrogen bonds.
I ran the command with 3-4.5 angstrom distance with 10-100 frames but it shows 0 hbonds.
When I ran atominfo it shows charge for all atoms 0. The results shows 4 donors and 2 acceptors. Can this be a reason for no hbonds?
Am I doing something fundamentally wrong here?
Best Regards,
Baig Abdullah Al Muhit
PhD student/Graduate Teaching Assistant
Department of Civil and Environmental Engineering
School of Engineering
Vanderbilt University, Nashville, TN
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Received on Sat Jul 15 2017 - 17:30:02 PDT
