Hello Justin, I commented out line 151 and braces enclosing it.
# unless ($resn =~ /SOL/) { for (my $z=1; $z<=$nres; $z++) { if ($donors{$z} == $natom) { $donor_names[$z] = $name; $donor_resn[$z] = join('', $resn, $resnum); } elsif ($acceptors{$z} == $natom) { $acceptor_names[$z] = $name; $acceptor_resn[$z] = join('', $resn, $resnum); } } # } Following is the ouput: In the beginning of the file i had these : # Donor Acceptor % Exist. 0.040 ASP1 N 0.020 ASP1 N 0.020 ASP1 N 0.100 GLU11 OE1 0.020 GLU11 OE2 0.020 HIS13 O 0.040 GLN15 OE1 0.040 Following these i had below lines., in the same file: # Donor Acceptor % Exist. 0.040 ASP1 N SOL171 OW 0.020 ASP1 N SOL172 OW 0.020 ASP1 N SOL175 OW 0.100 ASP1 N SOL177 OW 0.020 ASP1 N SOL179 OW 0.020 . . . . SOL682 OW HIS13 O 0.020 SOL682 OW GLN15 OE1 0.020 SOL682 OW GLN15 NE2 0.040 SOL682 OW ALA21 O 0.020 SOL682 OW GLU22 OE1 0.140 Kind regards, chetan. ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 13 December 2010 19:54 To: Gromacs Users' List Subject: Re: [gmx-users] HBOND probability Poojari, Chetan wrote: > Hello Justin, > > I commented out the lines from 151-161 > > # unless ($resn =~ /SOL/) { > # for (my $z=1; $z<=$nres; $z++) { > # if ($donors{$z} == $natom) { > # $donor_names[$z] = $name; > # $donor_resn[$z] = join('', $resn, $resnum); > # } elsif ($acceptors{$z} == $natom) { > # $acceptor_names[$z] = $name; > # $acceptor_resn[$z] = join('', $resn, $resnum); > # } > # } > # } > > > > I am ending up with the similar output. > Please comment out *just* the unless line (151) and the brace that encloses it, not the entire section. Otherwise, I suspect that nothing actually happened. That's the entire pattern matching operation there. Without it, the script probably doesn't do anything at all. -Justin > > > > 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 19:06 > To: Gromacs Users' List > Subject: Re: [gmx-users] HBOND probability > > Poojari, Chetan wrote: >> 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?? >> >> > > The script does not process hydrogen bonds involving SOL. The reason is that > the atom numbering goes haywire if you have too many waters and the output > doesn't make sense any more. > > If you need to analyze anything involving SOL, just take out the "unless" > statement on (or around) line 151 and the closing brace a few lines later. I > haven't tested that, but it should be the only thing keeping SOL from being > considered. > > -Justin > >> 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 >> > > -- > ======================================== > > 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 > -- ======================================== 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? 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