[AMBER] hbond analysis with CPPTRAJ

From: Baig abdullah Al muhit <bamuhit.yahoo.com>
Date: Sun, 16 Jul 2017 15:19:19 +0000 (UTC)

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 Sun Jul 16 2017 - 08:30:02 PDT
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