Sir, I tried extracting water using trjconv with the ndx file generated using g_hbond. The water I was looking for was within 2Ang from Magnesium atom, according to g_hbond -contact. but whatever trjconv extracted was 122..Ang away.
there were 2 chains, in 1 case correct water was extracted but in other case it was very far from Mg. Any suggestions are welcome. Regards Kavya On Thu, Feb 13, 2014 at 9:14 PM, Kavyashree M <[email protected]> wrote: > Dear Sir, > > Yes I can try with trjconv..!! Thank you for the suggestion! > > Regards > Kavya > > > On Thu, Feb 13, 2014 at 4:55 PM, Erik Marklund < > [email protected]> wrote: > >> Hi, >> >> I see. Can't trjconv extract the waters for you? >> >> Kind regards, >> Erik >> >> >> On 13 Feb 2014, at 11:10, Kavyashree M <[email protected]> wrote: >> >> > Dear Sir, >> > >> > For extracting specific waters involved in Hbond from the pdb I am using >> > a small script wherein i have to use the only information given in the >> index >> > file, generated from g_hbond, that is the atom number. so I am not clear >> > with it even now. Also the same problem is there with the residue >> numbering >> > of SOL in the, maximum is 9999 and the it restarts with 0. >> > >> > I still did not get your suggestion sir, please excuse my ignorance. >> > >> > Regards >> > kavya >> > >> > >> > On Thu, Feb 13, 2014 at 3:33 PM, Erik Marklund >> > <[email protected]>wrote: >> > >> >> Hi Kavya, >> >> >> >> Most (all?) gromacs tools ignore the atom indices in the PDB file >> anyway, >> >> so what you intend to do is straightforward. >> >> >> >> Kind regards, >> >> Erik >> >> >> >> On 13 Feb 2014, at 06:30, Kavyashree M <[email protected]> wrote: >> >> >> >>> Dear users, >> >>> >> >>> I was analysing the hydrogen bonding interaction of proteins and water >> >>> in a simulation and was trying to extract specific water that forms >> hbond >> >>> using matrix and index files generated by g_hbond. >> >>> >> >>> But I found that the index file created using g_hbond has continuous >> >> water >> >>> labels byt the pdb file of the system from the same trajectory does >> not >> >>> have continuous labeling, eg, max atom number of water(SOL) is 99999 >> and >> >>> then >> >>> it restarts from 0, similarly maximum residue label of water (SOL) is >> >> 9999, >> >>> then it restarts from 0. >> >>> >> >>> So if I want to use the number (of SOL) in index file generated from >> >> hbond >> >>> to extract respective atom in pdb file will be wrong. Kindly suggest >> me a >> >>> way out >> >>> of this. >> >>> >> >>> Thank you >> >>> Regards >> >>> Kavya >> >>> -- >> >>> Gromacs Users mailing list >> >>> >> >>> * Please search the archive at >> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> >> posting! >> >>> >> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >>> >> >>> * For (un)subscribe requests visit >> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> >> send a mail to [email protected]. >> >> >> >> -- >> >> Gromacs Users mailing list >> >> >> >> * Please search the archive at >> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> >> posting! >> >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> * For (un)subscribe requests visit >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> >> send a mail to [email protected]. >> >> >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to [email protected]. >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to [email protected]. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
