[gmx-users] Water naming

[Kavyashree M]

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
<erik.marklund at chem.ox.ac.uk>wrote:

> Hi,
>
> I see. Can't trjconv extract the waters for you?
>
> Kind regards,
> Erik
>
>
> On 13 Feb 2014, at 11:10, Kavyashree M <hmkvsri at gmail.com> 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
> > <erik.marklund at chem.ox.ac.uk>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 <hmkvsri at gmail.com> 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 gmx-users-request at gromacs.org.
> >>
> >> --
> >> 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 gmx-users-request at gromacs.org.
> >>
> > --
> > 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 gmx-users-request at gromacs.org.
>
> --
> 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 gmx-users-request at gromacs.org.
>