OK, I see the issue now - in retrospect I should have caught this
sooner. The problem is that the "generic" mask will only search for
*solute* hydrogen bond donors/acceptors; this is stated in the manual:
[<mask>] Atoms to search for solute hydrogen bond donors/acceptors.
The way to get around this is to explicitly specify donor and acceptor
atoms with the 'donormask' and 'acceptormask' keywords, e.g.
hbond donormask :HOH acceptormask :HOH./O out hbond.dat avgout hbavg.dat
Hope this helps,
-Dan
On Thu, Jul 20, 2017 at 9:34 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi, thanks for the files and sorry for the delay (I've been out sick
> for two days). I'll check this out and get back to you soon.
>
> -Dan
>
> On Mon, Jul 17, 2017 at 5:19 PM, Baig abdullah Al muhit
> <bamuhit.yahoo.com> wrote:
>> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> -------------------------
> 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
--
-------------------------
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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Received on Thu Jul 20 2017 - 07:30:03 PDT
