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
>
>
>
>
> _______________________________________________
> 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
Received on Thu Jul 20 2017 - 07:00:03 PDT
