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. > > > ------------------------------------------------------------------------------------------------ > ------------------------------------------------------------------------------------------------ > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), > Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > ------------------------------------------------------------------------------------------------ > ------------------------------------------------------------------------------------------------ -- ======================================== 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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists