Re: [AMBER] hbond analysis with CPPTRAJ

From: Baig abdullah Al muhit <bamuhit.yahoo.com>
Date: Sun, 16 Jul 2017 16:01:37 +0000 (UTC)

Hello Hai,
I had problems on my end when sending out the emails, so I wasn't sure if the email was going through or not. Sorry for that.
Baig

On Sunday, July 16, 2017, 10:55:32 AM CDT, Hai Nguyen <nhai.qn.gmail.com> wrote:

Please do not send your email 3 times like this. You don't get any
reply yet because it's weekend.

Hai

On Sun, Jul 16, 2017 at 11:19 AM, Baig abdullah Al muhit
<bamuhit.yahoo.com> wrote:
> 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 - 09:30:02 PDT
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