Just FYI: You can always check that in mailing list archive (normally
updated after 1 day I guess).
http://archive.ambermd.org/201707/
(see the bottom)
Hai
On Sun, Jul 16, 2017 at 12:01 PM, Baig abdullah Al muhit
<bamuhit.yahoo.com> wrote:
> 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 - 10:00:03 PDT
