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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@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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