[gmx-users] HBOND probability

[Poojari, Chetan]

Hello Justin,

As suggested i did remove the chain identifiers, so i do get residue numbers in my output. But the end result is still the same.

While choosing 2 groups to create index file, i choose protein as my first group and sol as my second group. (I choose the entire protein and solvent group as I wanted to know the protein residues involved in hydrogen bonding with the water molecules over time)

This is how my index file looks which is generated from  g_hbond. (retained only hbonds....)

[ hbonds_Protein-SOL ]
      1      2   7094
      1      2   7097
      1      2   7106
      1      2   7112
.
.
   7088   7089      8
   7088   7089      9
   7088   7089     24
   7088   7089     67
   7088   7089     73
   7088   7089     84



Summary.dat file contains: 
Donor	          	  Acceptor	             % Exist.
          	          	          	          	     0.040
      ASP1	         N	          	          	     0.020
      ASP1	         N	          	          	     0.020
      ASP1	         N	          	          	     0.100

                                       GLU3     OE2	     0.020
          	          	       ARG5	   O	     0.020
          	          	        HIS6	NE2	     0.020


Please can i know what might be the problem here??



Kind regards,
chetan



________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
Sent: 13 December 2010 13:37
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] HBOND probability

Poojari, Chetan wrote:
> Hello Justin,
>
> I wanted to find the probability of hydrogen bond formed between my peptide and water molecules over time. So I used your plot_hbmap.pl script.
>
> As mentioned in the script file, my index file contained atom numbers only from the  [hbonds...] section, rest were deleted.
>
> Heres my short output after running the script:
>
> #    Donor                        Acceptor                   % Exist.
>                                                                      0.004
>       ALAA               N                                           0.004
>       ALAA               N                                           0.016
>       ALAA               N                                           0.012
>       ALAA               N                                           0.008
>                                       ALAA               O           0.008
>                                       ASNA      OD1          0.012
>                                       GLYA               O           0.008
>                                       ALAA               O           0.008
>
>
>
> Please can I know if this is the expected output from the script ??? if not please can I know what might be wrong in my input ????
>
>

This is absolutely not the correct output.  Probably your index file is not
correct.  Also note that if you want proper residue names/numbers, you need to
use a .pdb file that does not have chain identifiers.

-Justin

>
> Kind regards,
> chetan.
>
>
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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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