Sir, I realise it may be due to the pbc. Its difficult to bring it near Mg with any of -pbc mol/centre etc.. calculations are fine but visualisation is difficult.
Regards Kavya On Sun, Feb 16, 2014 at 12:29 PM, Kavyashree M <[email protected]> wrote: > 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-usersor >>> >> 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].
