Hello Dr. Daneil,
Thank you for replying. Here are my PDB file with another water PDB file I followed from online. My file's name is wat.pdb. However, I could find 1 hydrogen bond with wat.mol2 file but not with PDB file. I am sending you the mol2 file also.
On Monday, July 17, 2017 12:23 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
Hi,
Can you send me off-list your PDB flie? It appears to be improperly
formatted. There appears to be an extra column of numbers before the
residue name. Also, nothing after the atom name is in the correct
column, but I'm not sure if that's a copy/paste artifact or not.
-Dan
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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> AMBER.ambermd.org
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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- application/vnd.palm attachment: wat.pdb
Received on Mon Jul 17 2017 - 14:30:02 PDT
