[gmx-users] Water naming

[Kavyashree M]

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 <hmkvsri at gmail.com> 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 <
> 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
>> >>> --
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